Highlights of the Annual Lake Committee Meetings Great Lakes Fishery Commission proceedings held in Ypsilanti, MI

Inland Seas Angler GREAT LAKES BASIN REPORT Special Report Lake Ontario A Publication of the Great Lakes Sport Fishing Council May 2009 http://www.great-lakes.org Vol. 20, No. 7 Highlights of the Annual Lake Committee Meetings Great Lakes Fishery Commission proceedings held in Ypsilanti, MI This third of a series of annual special reports is an extensive summary of the Lake Ontario annual Lake Committee. These Lake Committee reports are from the annual Lake Committee meetings hosted by the Great Lakes Fishery Commission of March 2009. We encourage reproduction with appropriate credit to the GLSFC and for the agencies involved. The other Lake Committee reports will be released shortly. Our thanks to the folks at the USGS Great Lakes Science Center, GLFC, USFWS, Ontario MNR and New York DEC for their contributions in making these science documents available. While they are abridged and have been edited for brevity, we have submitted extensive information that gives an overview of the status, conditions and prognosis of the Great Lakes and our fish. We especially thank the following for their assistance in getting us the many electronic documents, graphs, tables and reports:, Steve LaPan, NYSDEC; Bob Adair & Heather Dawson, USFWS; and Michael Bur, Jackie Savino, USGS Great Lakes Science Center; and their respective support staffs. Thanks also to the Great Lakes Fishery Commission, its staff and Marc Gaden & Chris Goddard, for their efforts in again convening and hosting all the Lake Committee meetings in Ypsilanti, MI. Lake Ontario Index of Reports Status of Important Prey Fishes in the U.S. Waters of Lake Ontario, 2008 pgs 1-3 2008 Annual Report, New York DEC Lake Ontario Unit & St. Lawrence River pgs 4-6 Lake Ontario Fish Communities; Report of the Lake Ontario Management Unit pgs 7-21 Lake Trout Rehabilitation in Lake Ontario, 2008 pgs 22-24 Lake Trout Production and Stocking pgs 24-26 Management of Sea Lamprey in Lake Ontario pgs 26-27 Status of Important Prey Fishes in the U.S. Waters of Lake Ontario, 2008 Abstract The U.S. Geological Survey (USGS) and New York State Department of Environmental Conservation (NYSDEC) have cooperatively assessed Lake Ontario prey fishes each year since 1978. Bottom trawling has been conducted during spring to assess alewife, summer to assess rainbow smelt, and autumn to assess slimy sculpin. Twelve transects were established at roughly 25-km (15.5 mile) intervals along the U.S. shoreline (Fig. 1). Although each survey targets one species of fish, catches of non-target fishes are also tracked and they provide information on ecologically important changes in the fish community such as the resurgence of once abundant native species like deepwater sculpin or increasing abundance of recently introduced invasive species like round goby. In 2008, the number of trawl hauls made for assessment of alewife, rainbow smelt, and slimy sculpin totaled 255 94 during April 21 - May 7, 103 during May 27 - June 5, and 58 during October 14 November 4. The number of trawl tows made to assess alewife was about 10% below the 1978-2005 average due to adoption of informed allocation of sampling effort in 2006. Fig. 1 - Lake Ontario showing 12 transects sampled with bottom trawls. Transect names, west to east, are: Olcott, Thirty Mile Pt., Oak Orchard, Hamlin, Rochester, Smoky Pt., Sodus, Fair Haven, Oswego, Mexico Bay, Southwick, and Cape Vincent Status of Alewife in U.S. Waters Abstract Adult alewife abundance and biomass indices increased from 2007 and were 67% and 69% of long term means, respectively. Condition of adult alewives remained high and was similar to condition during 2004-2007. Abundance of age-1 alewife was higher than anticipated, given the low number of available spawners, and was 62% of the long

2 Great Lakes Basin Report Special Report term mean. In 2009, adult alewife abundance and biomass may decrease due to a small 2006 year class recruiting as age-3 fish, and will be highly influenced by survival of the large 2005 year class which will be age 4. Even though spawner biomass has increased from the extremely low levels in 2006 and 2007, the recruitment model predicts that the 2008 year class will likely be below average because of the long winter duration in 2008-2009. Status of Alewife In April May 2008, the abundance of adult alewife (age-2 and older) in U.S. waters of Lake Ontario was higher than during 2004-2007, and more similar to the index in 2003 (Fig. 2). The 2008 weight index was equal to 67% of the long-term mean, 27% of the record high of 1981, and 510% of the record low of 2006. The 2008 numerical index was equal to 69% of the long-term mean, 30% of the record high of 1989, and 622% of the record low of 2006. In the adult population, we anticipate a low percentage of age-2 fish from the weak 2006 year class, and that the population will be dominated by age-3 fish. However, at this time we have only completed age estimates to establish age-1 fish and do not have further quantitative analyses of the age structure of the population. The predicted weight in fall 2008 was slightly below that in 2007, which was the heaviest since 1979 (Fig. 4). During 2003-2008, condition in fall has been higher than in any other period since the late 1970 s. Elevated condition each fall during 2003-2008 suggests that the alewife population was not expanding to a level at which it would depress food resources, and that the relatively small alewife population in recent years was more in balance with production from Lake Ontario s lower food web than at any time during 1981-2002. Analyses are ongoing to evaluate environmental influences on alewife condition. Fig. 4 - Wet weight of a 165-mm (6.5 ) alewife in spring and fall, 1976-2008 (1 gram = 0.035 ounce) Strength of alewife year classes at age 1 is positively linked to nearshore water temperatures during May July and negatively linked to the number of days nearshore water is < 4 C (39 F) during the first winter after hatch. In 2008, the spawning stock increased above levels observed during 2006-2007 and back within the range of model prediction. Model output indicates that, at age 1, the 2008 year class could be over double the long term mean at best, but more likely will be <30% of the long term mean based on the anticipated long duration of winter in 2008-2009. Fig. 2 - Abundance indices for adult (age-2 and older) alewife in U.S. waters, late April early May 1978-2008 The numerical abundance index for age-1 alewife in 2008 (2007 year class) was equal to 652% of the numerical index in spring 2007 and was 62% of the long term mean, which falls within the range (36%-72% of the long term mean Fig. 3). Although yearling alewife are not fully recruited to our sampling gear, we consider the yearling abundance index a reliable indicator of year class strength because the indices are correlated with the catch Fig. 3 - Abundance indices for yearling alewife in U.S. waters, late April early May 1978-2008 Status of Rainbow Smelt Abstract The abundance index for age-1 and older rainbow smelt in 2008 was the lowest yet recorded in the 31-year time series. The number of age-1 rainbow smelt caught in 2008 was lower than values for 2005-2007, and is lower than the previous all-time low number of age-1 smelt caught in 2003. An unusually large 2003 year class followed by a relatively small 2004 year class appeared to signal a resumption of the alternating pattern in year class strength that had been intact during 1984-2000, but four small year classes in succession in 2004-2007 indicate another breakdown in the pattern. Larger and older rainbow smelt remain scarce in Lake Ontario. Although the rainbow smelt population has demonstrated considerable resiliency in the past, it is unclear if it will be able to rebound from these low levels of spawners and recruits as it did in 2003. Status of Rainbow Smelt Number and weight indices for adult rainbow smelt were the lowest in the 31-year time series (Fig. 5). Numbers and biomass of age-1 and older were markedly lower than in 2004 when the abundance indices were the highest since

Great Lakes Basin Report Special Report 3 1998 (Fig. 5). In 2008, the numerical index was around 6% of the value for 2004, and the weight index about 18% of the value for 2004. Fig. 5 - Catch of rainbow smelt (age-1 and older) with bottom trawls in U.S. waters, in late May-early June 1978-2008 Rainbow smelt year classes generally alternate between strong and weak in Lake Ontario, apparently due to cannibalism, primarily by yearling smelt on young-of-year. The alternating pattern was interrupted by two successive weak year classes in 1982-1983 and again in 2001-2002. However, an unusually large catch of yearling rainbow smelt in 2004 (2003 year class) followed by a relatively small catch of age-1 fish in 2005 (2004 year class) appeared to signal a resumption of the alternating pattern in year class strength that had been intact during 1984-2000. The age-1 rainbow smelt index in 2008 was the lowest recorded in the 31-year time series. Small year classes in 2004-2007 seem to represent another breakdown in the alternating pattern of year class success and will likely make it difficult for this population to rebound as it has in the past. 2004, 17 deepwater sculpins were caught in U.S. waters of Lake Ontario and 2 were caught in Canadian waters, and among these deepwater sculpins, young, small individuals were numerically dominant. Catches of deepwater sculpins in standard assessment catches and presence of small individuals continued in 2006 and 2007 (18 and 7, respectively. In 2008, we collected 30 deepwater sculpins (37-145 mm [1.5 5.7"]) at depths 75 170 m (23 558 ft), during joint USGS/NYSDEC assessment cruises. The 2008 catch is an increase from previous years, primarily due to the catch of 19 individuals during the slimy sculpin assessment. The increased catch of deepwater sculpin with the new net design further strengthens our assertion that the new net is more effectively targeting benthic fishes. The continued presence of juvenile deepwater sculpins in our assessments indicates that conditions for survival of young deepwater sculpins are favorable, perhaps because of reduced abundance of alewife, which have been linked to depression of deepwater sculpin in Lake Michigan, and benthic piscivores such as burbot and lake trout. Round Goby Round gobies are now found along the entire south shore of Lake Ontario, with the highest population densities in U.S. waters just east of the Niagara River mouth. It appears that round goby will inhabit profundal waters for at least six months of the year (October through April), and are capable of colonizing to depths of at least 150 m (492 ft. Status of Sculpins and Round Goby Abstract During 2008 standard assessment sampling, we caught 30 deepwater sculpins (37-145 mm [1.5 5.7 in]), continuing the recent trend of increased catches of this species, once thought to be extirpated from Lake Ontario. In 2008, both the abundance and biomass indices for round goby increased from 2007 values. Sculpins Slimy Sculpin In 2008 Slimy sculpins were more abundant at depths greater than 70 m at all transects, and more abundant at eastern transects than at central or western transects, but due to recent gear changes we are unable to quantitatively compare abundance in 2008 to previous years. Deepwater Sculpin Deepwater sculpin were abundant in Lake Ontario in the 1920 s and at least common into the 1940 s. By the mid 1960 s, they were rare and thereafter, some considered the population extirpated. A recent summary of deepwater sculpin records from literature, commercial fishing records, and fisheries surveys in Lake Ontario during 1960 2005 documents sporadic captures of deepwater sculpin through Fig. 6 - Catch of round goby with bottom trawls in U.S. waters shoreward of the 160-m (525 ft) bottom contour in late April - early May 2002-2008 (no round gobies were caught prior to 2002) Given the potential importance of the round goby as a member of offshore and nearshore fish communities in Lake Ontario, we developed preliminary abundance and weight indices (calculated in the same manner as those for alewife and rainbow smelt, as depth-stratified, weighted means) to track the abundance of round goby in 2005 (Walsh et al. 2006). The round goby number and weight indices show an exponential increase through 2005, followed by an apparent plateau in numbers (2005-2006) but continued increase in the weight index (Figure 2). In 2007 and 2008, the index for both numbers and weight increased again (Fig. 6). Our 2007 and 2008 estimates of round goby biomass now exceed that of rainbow smelt.

4 Great Lakes Basin Report Special Report 2008 Annual Report, New York DEC Lake Ontario & St. Lawrence River Units Executive Summary Sport Fishery Assessment A 2007 NY Statewide Angler Survey estimated that angler expenditures for fishing trips to Lake Ontario and its five largest tributaries were $114.5 million. The 2008 charter catch rate of Chinook salmon was the 6th highest in the data series. The six highest Chinook salmon catch rates occurred during the six most recent years (2003-2008). Charter catch rate for rainbow trout was the highest on record (104.6% higher than the 2003-2007 average), with improvements across the season and all regions of the lake. Total trout and salmon catch (127,799 fish) and harvest (79,159 fish) were dominated by Chinook salmon (43.6% and 44.9%, respectively) and rainbow trout (26.7% and 24.9%, respectively). Brown trout catch rates in the east were above average for most of the season (April-September), resulting in the highest estimated seasonal catch rate for that area in the 24 years surveyed. In 2008, total effort was an estimated 70,598 fishing boat trips. 0.15 0.1 0.05 Chinook salmon 0 85 89 93 97 '01 '05 85 89 93 97 '01 '05 0.1 0 0.1 Coho salmon Brown Trout 0 85 89 93 97 '01 '05 Fig. 1 Catch rate of charter boats, 1985-2008 An estimated 52,111 boat trips targeted trout and salmon in 2008 (73.8% of fishing boat trips). Trout and salmon fishing effort in 2008 was comparable to the 2003-2007 average, indicating no changes in effort targeting trout and salmon in recent years. The number of lampreys observed per 1,000 trout and salmon caught was estimated at 22.2 in 2008, a 29.5% decrease compared to the 2003-2007 average and comparable to the previous 10-year average. Total trout and salmon fishing success was comparable to the previous 10-year (1998-2007; -6.9%) and long-term (1985-2007) averages. During 2003-2007 anglers 0.3 0.2 0.1 0.15 0.1 0.05 0 0.1 Rainbow trout (Steelhead) 85 89 93 97 '01 '05 Lake Trout 0 85 89 93 97 '01 '05 Total Trout and Salmon 0 85 89 93 97 '01 '05 experienced some of the highest catch rates since the survey was initiated in 1985 (Chinook salmon: 2003-2007, Coho salmon: 2006-2007; and brown trout: 2003 and 2007). Fishing boat trips targeting smallmouth bass during the traditional open season (3rd Saturday in June through September 30 when the creel survey ends) was an estimated 12,786 in 2008, 36.3% below the 2003-2007 average. A regulation change, effective October 1, 2006, permitted pre-season catch and release of smallmouth bass. Pre-season effort was low in 2007 (496 fishing boat trips and remained low in 2008 (367 fishing boat trips. In 2008, smallmouth bass catch and harvest remained low, possibly due to the impacts of round gobies on smallmouth bass distribution and vulnerability to angling. Prey Fish Assessments In spring 2008, the abundance and biomass of adult alewife (age-2 and older) in U.S. waters of Lake Ontario increased from 2007 and were 67% and 69% of long term means, respectively. Abundance of age-1 alewife was higher than anticipated, given the relatively low number of available spawners, and was 62% of the long term mean. During 2003-2008, alewife condition in the fall has been higher than in any other period since the late 1970 s suggesting that the alewife population was at a level that does not depress food resources, and that the relatively small alewife population in recent years was more in balance with production from Lake Ontario s lower food web than at any time during 1981-2002. Number Index (1000s) 12.0 10.0 8.0 6.0 4.0 2.0 0.0 1978 1981 USGS NYSDEC Number Weight (kg) 1984 1987 1990 1993 1996 1999 2002 2005 2008 120 100 Fig. 2 - Abundance indices for adult (age-2 and older) alewife in U.S. Waters, during late April early May, 1978-2008 The abundance index for age-1 and older rainbow smelt in 2008 was the lowest yet recorded in the 31- year time series. The number of age-1 rainbow smelt caught in 2008 was lower than values for 2005-2007, and is lower than the previous all-time low number of age-1 smelt caught in 2003. Larger and older rainbow smelt remained scarce in 2008. 80 60 40 20 0 Weight Index (Kg)

Great Lakes Basin Report Special Report 5 USGS successfully completed all scheduled tows in 2008. Standard assessment sampling by USGS/DEC during 2008 caught 30 deepwater sculpins, continuing the recent trend of increased catches of this species, once thought to be extirpated from Lake Ontario. In 2008, abundance and weight indices for the invasive round goby continued to increase. Gobies were first detected in 2002 and are now found along the entire south shore of Lake Ontario, with the highest population densities in U.S. waters just east of the Niagara River. Number Index 120 100 80 60 40 20 0 Round Goby in U.S. Waters of Lake Ontario USGS/NYSDEC Provisional Data Numbers Weight (g) 2002 2003 2004 2005 2006 2007 2008 Year 1400 1200 1000 Fig. 3 - Stratified mean catch of round goby with bottom trawls in U.S. waters, shoreward of the 160-m (525 ft) bottom contour in late April - early May, 2002-2008. (454 g = 1 lb) Coldwater Fisheries Management Fish stocking in the New York waters in 2008 included 798,780 Chinook salmon, 245,000 Coho salmon, 636,520 rainbow trout, 500,910 lake trout, 415,870 brown trout, and 49,470 Atlantic salmon. Lower than normal Chinook salmon stocking in 2008 (45%) was the result of low egg take and poor fertilization rates of eggs at NYSDEC Salmon River Hatchery in fall of 2007. High temperature and low flow in fall 2007 significantly reduced the numbers of adult salmon entering the hatchery and negatively affected survival of eggs. Stocking in 2009 is expected to be on target for 1.76 million Chinook. The 2008 mean length (36.5") and weight (21.3 lbs) of age-3 Chinook salmon in August, as measured from the open lake boat fishery, were 2.5% and 15.8% increases compare to 2007, respectively. Chinook salmon condition in 2008 improved dramatically from 2007 levels. The mean weight of age-1 Chinook males (jacks) sampled in 2008 increased markedly from those Weights of age-2 and age-3 Chinook salmon of both sexes also increased from the record lows observed in 2007 but remained below their respective long term averages. Age-2 fish were about 1 pound (males) and 1.8 pounds (females) below their long-term averages. Age-2 fish were significantly lighter than 8 (males) and 10 (females) of the previous 22 years sampled. Age-3 fish of both sexes were about 1 pound below their long-term averages. Age-3 fish were significantly 800 600 400 200 0 Weight Index (g) POUNDS. lighter than 9 (males) and 13 (females) of the previous years sampling. 24 22 20 18 16 14 12 10 1986 1989 1992 1995 1998 2001 2004 2007 YEAR AGE 3 M AGE 3 F AGE 2 M AGE 2 F Fig. 4 - Weights of male and female Chinook salmon ages 2-3 at Salmon River Hatchery 1986-2008 Steelhead are sampled in the spring and, unlike Chinook and Coho salmon, do not reflect growth during the 2008 growing season. Weights reported here reflect conditions prior to and including 2007. Weights of age-3 fish of both sexes were slightly under a pound lighter than their respective long term averages. Age-4 males were the lightest on record and significantly lighter than those sampled in 15 of the 20 previous years in the data set. Age- 4 females were the fourth lightest on record and 1.1 lbs below their long term average (Fig. 6). The females were not significantly heavier than those sampled in any of the previous years but they were significantly lighter than those sampled in 11 of the previous 20 years. POUNDS. 12 11 10 9 8 7 6 5 4 AGE 4 M AGE 4 F AGE 3 M AGE 3 F 1988 1991 1994 1997 2000 2003 2006 YEAR Fig. 5 - Mean weights of Washington steelhead ages 3-4 at Salmon River Hatchery 1988-2008 Since the institution of seasonal base flows in the Salmon River, a dramatic increase in natural reproduction of Chinook salmon continues to be documented. The 2008 year class of wild Chinook salmon appears to be very weak with a mean peak catch of only 49 YOY Chinook per haul during the last week of May and the first two weeks of June. Catches throughout the survey were well below average (18% of the long-term mean) and the peak occurred later and was more prolonged than normal. Mean Salmon River flow during the preceding October continues to be an

6 Great Lakes Basin Report Special Report important factor explaining year class strength and the extremely low flows and warm temperatures of October 2007 produced a record low year class. The eleventh year of pen-rearing steelhead trout and Chinook salmon along the New York shoreline was very successful due to low fish mortality at all sites, and a relatively high percentage of fish reaching target weights. A total of 35,000 Washington strain steelhead was raised at four pen sites, comprising 7% of NYSDEC Lake Ontario rainbow trout/steelhead stocking allotment in 2008. Four pen-rearing sites raised a total of 191,190 Chinook salmon, representing 23% of NYSDEC 2008 Chinook stocking allotment. Lake Trout Restoration In 2008 the juvenile lake trout survival index remained low, similar to recent years, and was 88% below the average for the 1983-1989 year classes. A total of 407 lake trout were captured in the September 2008 adult lake trout gill net survey. The 2008 CPUE (5.2) of adult fish increased 52% from 2007, however, was 70% below the 1986-1998 mean and 53% below the 1999-2004 mean. The 2005-2008 mature lake trout CPUEs were similar to the 1982 and 1983 values which pre-dated effective sea lamprey control and recruitment from the first large stocking in 1979. Sea lamprey wounding rates on lake trout remain much lower than pre-1985 levels, but were above the target level of two A1 wounds per 100 fish for eight of the last twelve years. A1 wounding rate in 2008 fell below the target level to 1.47 wounds per 100 fish. CPUE 25 20 15 10 5 0 1980 1982 1984 1986 1988 1990 Fig 6 Catch per unit effort of immature and mature lake trout, 1980-2008 1992 In 2008, one naturally produced (wild) age-2 (278 mm, 10.9") lake trout was caught during bottom trawling. Survival of naturally produced lake trout to the fingerling stage in summer and fall occurred each year during 1993-2006 representing production of 14 consecutive year classes. Condition of adult lake trout (weight of a 700 mm (27.6") total length fish) in 2008 (3676.0 g, 8.1 lb) increased from 2003-2006 values, and was equivalent to the 1996-1999 mean (3679.6g, 8.1 lb; the highest values in the data series). In 2008, lake trout harvest (2,875) and harvest rate were the 2 nd lowest values recorded and catch (6,757) was the lowest 1994 1996 1998 Mature Male Mature Female Immature 2000 2002 2004 2006 2008 recorded. Relatively poor fishing for lake trout in 2008 was likely due, in part, to both the declines in adult population size since 2004 and the relatively good fishing quality for Chinook salmon. Warmwater Fisheries A total of 55,111 fingerling walleye were stocked into Lake Ontario embayments and the Lower Niagara River. Catch-per-unit-effort (CPUE) of warmwater fish in the 2008 Eastern Basin index gill netting survey was 74.5% and 94.4% higher than previous 5-year (2003-2007) and 10-year (1998-2007) averages, respectively. This was the highest CPUE since 1992 and is primarily attributable to increased CPUE of white perch (highest since 1991) and yellow perch (highest since 1984). Smallmouth bass abundance in the Eastern Basin as measured in index gill nets was 14.9% below the 2005-2006 average (highest CPUEs observed since 1994), however, was 120.4% higher than the 2000-2004 average (the period of lowest CPUEs on record). Recent improved smallmouth bass growth and condition continued in 2008 with record or near record high mean length-at-age for all ages 2-10, and record high condition for most length increments examined. Yellow perch abundance in 2008 was the highest since 1984, a 129.5% increased compared to the 1989-2006 average and a 74.1% increase compared to the 2003-2007 average. Walleye abundance in 2008 was 23.3% and 35.5% above previous 5-year and 10-year averages, respectively. The strong 2003 yearclass represented 18.8% of the 2008 catch (mean length=22.8"). White perch abundance was more than 6-fold higher than the previous 5-year average and the highest since 1991. Lake sturgeon was collected in the Eastern Basin assessment in 11 of the last 14 years suggesting improvements in population status. Round gobies first appeared in the Eastern Basin assessment in 2005 in both gillnet catches and smallmouth bass diets. Goby occurrence in predator diets increased each year since, and in 2008, were found in one walleye stomach, two northern pike stomachs, and 51.0% of non-empty smallmouth bass stomachs (208 stomachs examined). C P U E 140 120 100 80 60 40 20 0 Smallmouth bass Yellow Perch White Perch 76 79 82 85 88 91 94 97 '00 '03 '06 Fig. 7 Catch per unit effort of smallmouth bass, yellow and white perch in the Eastern Basin gillnetting program, 1976-2008

Great Lakes Basin Report Special Report 7 Lake Ontario Fish Communities; Lake Ontario Management Unit Report Forward During 2008, the Lake Ontario Management Unit (LOMU) worked closely with Canadian federal agencies, provincial governments, various U.S. federal and state agencies and non-government partners to develop and implement plans to protect and restore American eel, lake trout, and Atlantic salmon. Similar plans are being drafted for the conservation of lake sturgeon and for the restoration of deep-water coregonids. LOMU worked with partners to understand the spread and initial effects of a new invader, the bloody red shrimp. LOMU provided input to Districts about projects with fish habitat implications. LOMU continued to provide observations to surveys of occurrences of fish diseases and advanced analysis of the effects of disease outbreaks on wild fish. Also in 2008, a new Fisheries Management Zone 20 Advisory Council was established for the lake and river bringing together a group of volunteers with interests in recreational fishing, commercial fishing, and the environment to assist the Lake Manager with advice and recommendations about recreational fisheries. These liaison committees are the central elements to a strong communications network that helps us make sound resource management decisions (e.g., setting sport fishing regulations, commercial fishing quotas, stocking levels, and fisheries management objectives). Status of Major Species The following is an overview of the status of major species in Ontario waters of Lake Ontario for 2008. Chinook salmon Condition of large Chinook salmon in the Credit River in 2008 continued to be lower than most years since 1989, and was similar to 2006 and 2007. Although current prey fish populations still support this top predator, the long term stability of the fish community remains in question. Rainbow Trout Counts of wild rainbow trout at the Ganaraska River fishway have continued to be stable from 1998-2008. Condition of rainbow trout in the Ganaraska River in 2008 remained good; it declined but was only 5% below the long term average. Sea lamprey marks on rainbow trout are a concern as they have increased to the highest level observed, including the 1970s before sea lamprey control. Lake Trout The abundance of adult lake trout remains low after a period of decline that began in the 1990s, and which is attributed to the combination of decreased survival of the stocked juveniles and reduced stocking numbers. In recent years the early survival appears to be improving again. Lake Whitefish Abundance of Lake Whitefish in assessment gillnets is very low relative to that of the 1990s. Many strong year-classes produced in the late-1980s and early 1990s are aging and declining in both assessment gillnets and commercial gear. Reproductive success was very low after the mid 1990s until a strong year-class was produced in 2003. Growth of these young fish is very slow (e.g., age-5 fish from 2003 year-class were 22% less in fork length and 58% less in body weight compared to age-5 fish from the early 1990s) and age-at-maturity is delayed by at least two years. In 2008, age-5 fish from the 2003 yearclass were the most abundant age-class in the assessment gillnets (22% of the catch). More recent catches of age-0 fish in assessment bottom trawls suggested that poor year-classes were produced in 2004, 2006, 2007 and 2008 but another relatively strong year-class was produced in 2005. The condition of Lake Whitefish caught in summer assessment gillnets improved after the mid to late 1990s but condition of fish caught during the fall remained low. Commercial lake whitefish harvest increased in 2008 to 68,072 lbs. Northern Pike Northern pike, while not abundant in the open-waters of Lake Ontario are common in many embayment and nearshore areas. Catches in upper Bay of Quinte assessment gear did not meet the Bay of Quinte Fisheries Management Plan (BQFMP) target. The plan called for catches to be at least as high as those seen during 2002-2006 but catches have dropped. American Eel The total number of eel migrating upstream at the ladders, located at the Moses-Saunders Hydroelectric Dam on the St. Lawrence River, during 2008 was twice what has been observed in recent years. While this development is encouraging, the abundance of eel entering the upper St. Lawrence River and Lake Ontario is still less than 3% of the migrations observed in the early 1980s. Even with the closure of the commercial (2004) and sport fisheries (2005), the abundance of yellow eel in the Lake Ontario/upper St. Lawrence River ecosystem remains low. The OMNR worked with Ontario Power Generation to stock eels into the upper St. Lawrence River and the Bay of Quinte (see Section 7.1) to help maintain eels in this system and to improve biodiversity. In addition, Ontario is continuing to work with management agencies in other jurisdictions, and other stakeholders, including the Ontario Power Generation, Hydro Quebec, local commercial fish harvesters and the New York Power Authority, to encourage the safe passage of eels around hydro dams and mitigate barriers to migration. A pilot project was undertaken to trap large yellow eels in the Lake Ontario upper St. Lawrence River and release them below all barriers to downstream migration in the St. Lawrence. Preliminary results of this project suggest that some of the transported eel do migrate out of the St. Lawrence River system towards the spawning grounds. It is hoped that these actions will contribute to the fecundity of the global spawning stock. Sustainable management practices throughout the range of this panmictic species in North America will be required to restore eel abundance.

8 Great Lakes Basin Report Special Report Smallmouth Bass Smallmouth bass, having declined in abundance during the 1990s, remain at low to moderate levels in the nearshore areas. Smallmouth catches in Bay of Quinte assessment gear did not meet the target established in the Bay of Quinte Fisheries Mgmt Plan (BQFMP). The plan called for an increase in catches relative to a mean catch threshold established from samples taken during the 2002-2006 sampling period. Catches in 2008 did not change from those of the target period. Largemouth Bass Largemouth bass abundance increased in the Bay of Quinte following increases in water transparency and aquatic vegetation in the late 1990s. Their current level of abundance exceeds that of walleye in nearshore areas, and meets the BQFMP target for maintaining catches relative to those seen during 2002-2006. Largemouth bass are moderately abundant in other embayment areas of Lake Ontario. Prey Fish After a record low level in 2007, the abundance of yearlingand-older alewife increased in 2008, but remained in line with the generally low levels observed since 2003. Similarly, there was a modest increase in the population of yearling-and-older rainbow smelt, but the abundance remains low, at levels observed since the early 2000s. Three-spine stickleback abundance decreased dramatically in 2006-2007, prompting concerns for the future abundance of this species. Due to technical difficulties, their status could not be assessed in 2008. Round Goby Round goby invaded Lake Ontario in the late 1990s and first appeared in routine Bay of Quinte assessment bottom trawls in 2001 and gillnets in 2002. Goby distribution expanded to include all areas of eastern Lake Ontario and the Bay of Quinte to depths of at least 36 m by 2006. Overall goby abundance appears to have peaked in the Bay of Quinte and possibly stabilizing Lake Ontario. Panfish Panfish, particularly pumpkinseed, bluegill and black crappie, increased after re-establishment of submerged aquatic macrophytes in the Bay of Quinte. These events were associated with post dreissenid mussel invasion in the 1990s. Panfish are also common in other Lake Ontario embayments and nearshore areas. Yellow Perch Yellow perch is one of the most common species in the nearshore areas. Their current abundance levels in Lake Ontario are low to moderate compared to past levels. Yellow perch catches in 2008 generally exceeded BQFMP targets which call for maintaining catches relative to those seen during 2002-2006. Yellow perch commercial harvest decreased in Lake Ontario and increased in the St. Lawrence River. Yellow perch are currently, by far, the most valuable species in the commercial fishery. Walleye While abundance remains considerably lower than during the late 1980s and early 1990s, the eastern Lake Ontario/Bay of Quinte walleye population has been very stable since 2001. Further, recruitment indices, based on young of year catch in bottom trawls, indicate that a strong year-class was produced in 2003, and that average (i.e. average for the last ten years) year-classes were produced in 2004, 2005 and 2006. The 2007 yearclass index is the 3rd highest since 1995 and the 2008 year-class is the highest since 1994. Catches at age-1 in assessment gillnets suggest that the 2004 year-class is weaker and the 2005 year-class stronger than first indicated by the trawls. The 2003 and 2005 year-classes also figure prominently in nearshore trapnet catches including in other areas of Lake Ontario. Based on these recent recruitment levels, the walleye population should remain stable or increase, at least through the next few years. Current walleye status meets or exceeds BQFMP targets that call for a maintenance of walleye catches at 2002-2006 levels. Index Fishing Projects Ganaraska Fishway Rainbow Trout Assessment The fishway on the Ganaraska River at Port Hope has been in operation since 1974. During 2008, rainbow trout were counted and sampled for length, weight and age during the spring spawning run. The count of rainbow trout in the spring run has been relatively stable since 1998, and in 2008 was estimated at 4,713 fish, about one-third peak abundances observed during the late 1980s (Fig. 1). The body condition of rainbow trout in Lake Ontario was calculated as the estimated weight of a 635 mm (25") fish at the Ganaraska River. In 2008, the weights of male (2,889 g) and female (3,012 g) rainbows were not different than observed during 2007 and were below the long-term average for the data. In 2008, sea lamprey marks on rainbow trout in the Ganaraska River were the highest observed (Fig. 2), and were more than five times higher than the average for 1990-2003. The marking rates from 2004-2008 were similar to levels in the 1970s (Fig. 2). A high incidence of A1 and B1 marks since 2004 indicated very recent attacks relative to rainbow trout migrating into the Ganaraska River. Fig 1 - Estimated upstream counts of rainbow trout at Ganaraska River fishway at Port Hope, during April & May, 1974-2008

Great Lakes Basin Report Special Report 9 Fig 2 -Trend in sea lamprey marks on rainbow trout in April, 1974 To 2008, at the Ganaraska River fishway, in Port Hope, Ontario 2007 (2,689 eels) but similar to that observed during 2006 (8,960 eels). At the 3-yr old Moses eel ladder, a total of 25,932 eels transited the passage facility which was operated between July 1 and November 1, 2008. During 2006, the first year of operation for the Moses ladder, the numbers at the two eel ladders were very similar. During both 2007 and 2008, almost 4-times more eels were estimated to transit the Moses ladder at the south end of the dam compared to the Saunders ladder. Combined, 32,330 eels passed the two ladders during 2008. This number is approximately double what was observed in 2006 (17,144) and 2007 (14,204) and continues the trend of increasing numbers since 2001. However, the numbers migrating upstream are still less than 3% of the numbers of eel observed during the early 1980s. Large Salmonid Predation Impacts on Postsmolt Salmonids Fifteen fish species were observed in the samples, an increase from 11 species in 2008. Significantly, two new species were Atlantic salmon and rainbow trout and these were only observed in the new 4 m depth zone (Table 1). As well, rainbow smelt were observed only in the 13 mm gillnet panels. Accordingly, the modifications to the program in 2008 proved very instructive. In addition, walleye were observed in 2008 for the first time, and were observed in greater abundance in the shallower depths of the east. Catches in bottom gillnets were dominated by two major prey species: alewife, and round gobies (Table 1). Suspended nets caught only alewife and round gobies. Catches of round gobies (a benthic species) in a single suspended sample suggests the net had sagged down and touched the bottom. The fork length of salmon and trout indicated the presence of juveniles (> 275 mm) and larger, potential predators of the juveniles. However, gillnet selectivity increases with fish size and so the juveniles are likely underrepresented in our samples. Fig 3 - Length of eel migrating upstream through eel ladder located at Saunders Hydroelectric Dam, 1975-2008 Eastern Lake Ontario and Bay of Quinte Fish Community Middle Ground Seven species were caught at Middle Ground in 2008. The most abundant species were yellow perch, white sucker, northern pike, alewife and walleye. Yellow perch were more abundant in 2008 than in 2007 but less abundant than the average during 1992-2008. White sucker, northern pike and brown trout were more abundant in 2008 than their long-term averages. Walleye were less abundant than their long-term average. Alewife, a species that was moderately abundant in the early to mid-1990s but not been caught in the past five years, reappeared in the 2008 catch at Middle Ground. TABLE 1 - The average catch per standard gillnet in bottom gillnets in central Lake Ontario, during May 2008 Saunders Hydroelectric Dam Eel Ladder Monitoring The Saunders eel ladder, operated by Ontario Power Generation on the Canadian side of the Moses-Saunders Power Dam, has provided counts of American eels migrating upstream since 1974 This year s count at the Saunders ladder is somewhat higher than observed during Fig 4 - NE Lake Ontario and Bay of Quinte fish community index gillnetting locations

10 Great Lakes Basin Report Special Report Northeast Seventeen species were caught in the Northeast Lake Ontario gillnets in 2008. The most abundant species were alewife, round goby, yellow perch, rock bass, and brown trout. Of these species, alewife, rock bass and brown trout were more abundant in 2008 than the 1992-2008 average while round goby and yellow perch were less abundant. The cold-water benthic species, lake trout, lake whitefish and round whitefish, declined markedly over the 1992-2008 time period. Round goby, caught for the first time in 2003 is now, along with yellow perch, the second most abundant species in the northeast region. Rocky Point (deep sites) Five species, alewife, lake trout, Lake Whitefish, rainbow smelt and slimy sculpin were caught at the Rocky Point deep sites in 2008. Alewife were more abundant in 2008 than in any other year since 1997. rock bass, walleye, and white perch. Of these species alewife and rock bass were more abundant in 2008 than the 1992-2008 average; the other species were less abundant. Round goby, which were caught for the first time in 2002 and which had increased to a high abundance level by 2004, have subsequently declined to very low levels. Species Highlights Lake Whitefish Eighty-six lake whitefish were caught in the 2008 index gillnets up from 51 the year previous and 28 in 2006. 22% of these fish were age-5 from the 2003 year-class. These age-5 fish were an average of 369 mm fork length and 592 g in weight. 56% of these age-5 fish were classified as mature. Lake whitefish condition appears to have stabilized at a level (e.g. a 480 mm fish is approximately 3 lb) lower than that observed in the early 1990s but significantly higher than that in 1996 and 1997 (Fig. 3). Kingston Basin (nearshore sites) Fourteen species were caught in Kingston Basin nearshore nets in 2008. Similar to 2007, the most abundant species were alewife, yellow perch, walleye, round goby, and rock bass (Table 2). Alewife and rock bass were more abundant in 2008 than their long term averages; yellow perch, walleye and round goby were less abundant. Round goby declined to its lowest level since being caught for the first time in 2003. Burbot, which were caught each year from 1992-2004, have not been caught in the last four years. Kingston Basin (deep sites) Nine species were caught in Kingston Basin deep gillnets in 2008. The most abundant were alewife, lake trout, Lake Whitefish, yellow perch and brown trout (Table 3). The catches of each of these species was higher in 2008 than in 2007. Round goby, caught for the first time in 2004 at these deep sites, were not captured in 2008. Bay of Quinte Big Bay Thirteen species were caught in Big Bay gillnets in 2008. The most abundant species were white perch, yellow perch, walleye, freshwater drum and common white sucker. Of these species, all except freshwater drum were more abundant in 2008 than their 1992-2008 average. Brown bullhead have shown a steady decrease in abundance since 2001. Round goby, first caught here in 2003, have not been caught since 2005. Hay Bay Thirteen species were caught in Hay Bay gillnets in 2008. The most abundant species were yellow perch, white perch, white sucker, walleye and northern pike. Of these species, white perch and northern pike were more abundant in 2008 than the 1992-2008 average; while the others were less abundant. Round goby, having been caught each year from 2002-2005, were absent from the 2006-2008 catches. Conway Seventeen species were caught in Conway gillnets in 2008. The most abundant species were alewife, yellow perch, Walleye The age distribution of walleye showed a broad range of age-classes from age-1 to age-21. During the summer index gillnetting program young walleye were found in the Bay of Quinte (e.g., age-1 to age-5 fish comprised 87% of the Bay of Quinte walleye catch) while older walleye were present in eastern Lake Ontario (e.g., age-6 and older fish comprised 77% of the catches in the Kingston Basin). Of the young walleye, all ages were quite common indicating that year-class strength has been relatively strong and consistent in recent years. Older walleye, from many strong year-classes, were also abundant in eastern Lake Ontario. The 2003 year-class appears particularly strong in Lake Ontario. Female walleye begin to mature for the first time during the summer at age-3 to presumably spawn the following spring at age-4. Round Goby Only large round goby are susceptible to capture in assessments gillnets. Round goby first appeared in assessment gillnets in the northeast and Bay of Quinte in 2002, Kingston Basin nearshore sites in 2003 (depth range 7.5 to 27.5 m), and in Kingston Basin deep sites (depth about 30 m) in 2004. No round goby were captured to date at Middle Ground or the Rocky Point deep sites (40-140 m). In the Bay of Quinte, round goby abundance initially increased, peaked in 2004, and then decreased substantially over the next four years. In Lake Ontario, goby abundance increased until 2007 and then declined in 2008. Lake Trout The abundance of lake trout remains low, although increased catches were seen in the Kingston Basin. The current levels were reached around the year 2002, after a period of decline that began in the early 1990s, and which was attributed to reduced stocking levels combined with a decline in early survival of the stocked fish. Recently there appears to be improvement in the early survival which may lead to future increases in adult abundance.

Great Lakes Basin Report Special Report 11 Kingston Basin (nearshore sites) TABLE 2 - Species-specific catch per gillnet set in the Kingston Basin (nearshore sites), 1992-2008. The total number of species caught and gillnets set each year are indicated. Kingston Basin (deep sites) TABLE 3 - Species-specific catch per gillnet set in the Kingston Basin (deep sites), 1992-2008

12 Great Lakes Basin Report Special Report Age-0 yellow perch at six Bay of Quinte sites, 1992-2008 technical problems. Trawling is normally part of the hydroacoustic survey, providing data on species composition and biological attributes of the fish. The alewife population estimate for 2008 is 243 million yearling-and-older fish. This is an increase from the previous year, but in line with the general population levels seen since 2003 (Fig. 5). The 2008 population estimate translates into a biomass estimate of 8178 MT. TABLE 4 - Age-0 yellow perch at six Bay of Quinte sites, 1992-2008 Age-0 walleye at six Bay of Quinte sites, 1992-2008 Fig. 5 - Abundance and biomass of yearling/older alewife The rainbow smelt population estimate for 2006 was 216 million yearling-and-older fish, which translates into a biomass estimate of 1680 MT (Fig. 6). As with alewife, the 2008 smelt population estimate is higher than the previous year s estimate, but in line with the low levels observed in recent years. TABLE 5 - Age-0 walleye at six Bay of Quinte sites, 1992-2008 Round goby at 3 Ontario and 6 Bay of Quinte sites, 1992-2008 Fig 6 - Abundance and biomass of yearling/older rainbow smelt Table 6 - Round goby at three Ontario and six Bay of Quinte sites, 1992-2008 Lake-wide Hydroacoustic Assessment of Prey Fish The 2008 hydroacoustic survey was conducted from Jul 31- Aug 6, and consisted of five north-south shore-to-shore transects in the main lake, and one transect in the Kingston Basin. Midwater trawling was not possible in 08 due to Three-spine sticklebacks are another species assessed in the hydroacoustic surveys, albeit only from the catches in the midwater trawls that accompany the acoustic data collection. A sharp decrease in abundance of the sticklebacks was observed in 2006-2007, leading to concerns about the future levels of this species. Unfortunately the status in 2008 could not be assessed because we could not conduct midwater trawls. Nearshore Community Index Netting The provincial standard nearshore community index netting program (NSCIN) was adopted to sample the nearshore fish community beginning during 2001. In 2008, NSCIN was

Great Lakes Basin Report Special Report 13 conducted in five areas: Lake St. Francis (St. Lawrence River), the upper Bay of Quinte, Weller s Bay, Presq ile Bay, and Hamilton Harbor. Bluegill Bluegill were most abundant in the upper Bay of Quinte and least abundant in Lake St. Francis. Lake St. Francis Thirty-six trapnet sites were sampled from Aug 18-Sep 5. Nearly 3,400 fish comprising 16 species were captured. The most abundant species by number were brown bullhead (1,279), pumpkinseed (907), rock bass (472), yellow perch (220), white sucker (142) and black crappie (118). Of note, eight silver lamprey and seven American eel were caught. Bay of Quinte Thirty-six trapnet sites were sampled on the upper Bay of Quinte from Sep 8-26. Nearly 8,400 fish comprising 18 species were captured. The most abundant species by number were bluegill (5,728), pumpkinseed (653), black crappie (624), yellow perch (252), brown bullhead (231), largemouth bass (194) and white perch (155). Four species of redhorse were caught silver (18), shorthead (12), greater (3), and river redhorse (16) a species of special concern. Weller s Bay Twenty-four trapnet sites were sampled from Sep 16-26. Nearly 2,400 fish comprising 14 species were captured. The most abundant species by number were bluegill (835), rock bass (156), pumpkinseed (78), brown bullhead (63), largemouth bass (53) and smallmouth bass (48). Presq ile Bay Twelve trapnet sites were sampled from Sep 30-Oct 2. Over 700 fish comprising 14 species were captured. The most abundant species by number were brown bullhead (332), bluegill (147), pumpkinseed (63), rock bass (56) and largemouth bass (50). Hamilton Harbor The Hamilton Harbor NSCIN project was conducted in partnership with the Department of Fisheries and Oceans at Burlington. Twenty-four trapnet sites were sampled from Aug 11-22 with water temperatures ranging from 20.1-22.9 oc. Over 6,200 fish comprising 17 species were captured. The most abundant species by number were brown bullhead (4,544), white perch (837), channel catfish (382) and common carp (94). Of note was the capture of a single muskellunge, several large northern pike and a small rainbow trout. Smallmouth bass Smallmouth bass were present moderate abundance levels in Weller s Bay, Lake St. Francis and the upper Bay of Quinte but absent from the Presq ile Bay and Hamilton Harbor catches. Largemouth bass Largemouth bass were most abundant in the upper Bay of Quinte and Presq ile Bay areas, present at moderate levels in Weller s Bay and at relatively low levels in Lake St. Francis and Hamilton Harbor. Black crappie Black crappie were most abundant in upper Bay of Quinte, and Lake St. Francis, and uncommon in the other areas. Yellow perch Yellow perch were most abundant in the upper Bay of Quinte and Lake St. Francis, moderately abundant in Presq ile Bay and uncommon in Weller s Bay and Hamilton Harbor. Walleye Walleye were most abundant in the upper Bay of Quinte and Weller s Bay. Walleye were less common in Lake St. Francis and Presq ile Bay, and rare in Hamilton Harbor. The majority of walleye caught across the waterbodies were young--from age-1 to age-5 years. A few older fish were caught in all areas except Presq ile Bay. The most common age was age-5 (2003 year-class) followed closely by age-3 fish (2005 year-class). Length-at-age was similar and high in all areas except Weller s Bay where length-at-age was significantly lower. St. Lawrence River Fish Community Index Lake St. Francis Thirty-six sets were made. The nets were fished for approximately 24 hours. The overall catch was 1,755 fish comprising 14 species (summary in Table 7). Status of Selected Species Northern pike Northern pike were most abundant in Hamilton Harbor and least abundant in the upper Bay of Quinte. American eel Seven American eel were caught in Lake St. Francis but none was caught in the other areas. Pumpkinseed Were most abundant in Lake St. Francis and the upper Bay of Quinte and least abundant in Hamilton Harbor. Table 7 - Summary of catches per standard gillnet set in Lake St. Francis surveys 1984-2008

14 Great Lakes Basin Report Special Report The average number of fish per set was 48.9 which is the highest since the survey series began in 1984, and more than three times the low levels observed in 2002 (Fig. 7). The dominant species in the catch were yellow perch, rock bass, brown bullhead, common white sucker and smallmouth bass (Fig. 8). Fig. 10 - Catches of northern pike, Lake St. Francis, '84-'08 Fig. 8-2008 Species composition in Lake St. Francis Species Highlights Yellow perch rebounded in 2008. Previously, there has been a dramatic decline in the abundance of yellow perch between the start of the series in 1984 and 2002 (Fig. 9). The decline was especially evident in large perch (>220 mm) indicating increased mortality of older fish. The trend, however, was reversed in 2006, when large number of small perch was caught, and in 2008 the catches of both small and large perch were the highest since the start of the survey series in 1984. Northern pike remained relatively stable through the period of 1984-1992 (Fig. 10). A decline in abundance of small fish (<500 mm) was observed in 1994, followed by a sharp decline in abundance of all sizes in 2002. Smallmouth bass have increased in abundance in recent years the average catches in the 1998-2008 period were almost twice as high as those in 1984-1994 (Fig. 11), and the catches in 2008 were the highest since the start of the survey series in 1984. Walleye were caught in low and relatively stable numbers in the past, but in 2008 the catches of walleye increased to more than double the average numbers seen since the start of the survey series. Fig. 11 Catches, smallmouth bass and walleye, Lake St. Francis, 1984-2008 Credit River Chinook Assessment Growth, condition and lamprey marking of Chinook salmon were monitored during the fall spawning run in the Credit River at the Reid Milling dam in Streetsville. Chinook salmon were electrofished in the Credit River for spawn collection by the Ringwood Fish Culture Station. LOMU crews measured the fork length, weighed, and collected otoliths from Chinook salmon for ageing. The body condition was estimated for each sex as the weight of a 900 mm fish based on a general linear model. Fig. 9 - Catches of yellow perch, Lake St. Francis '84-'08 This pattern is the opposite of the one observed in yellow perch, and it suggests a recruitment problem. The levels over the past four surveys (eight years) have remained low, and given that the abundance of small pike declined more than ten-fold since the mid 1990s, further decreases in abundance of large pike can be expected. Condition (mean weight of a 900 mm fish) of male and female Chinook salmon in the Credit River in 2008 compared was not significantly different from 2007 and 2006, and remained among the lowest observed since 1989 (Fig. 12). In 2008, sea lamprey marks on Chinook salmon in the Credit River declined to very low levels (Fig. 13), similar to the early 1990s.

Great Lakes Basin Report Special Report 15 effort, catch and harvest values in 2008 were similar to values observed after 2000. Numbers of walleye caught and harvested per hour by anglers targeting walleye were 0.187 and 0.124 respectively; somewhat low relative to recent years (Table 8). Over 40% of harvested walleye were age-3 (Fig. 14) from the 2005 yearclass. Fig. 12 - Weight of 900 mm Chinook salmon in the Credit River, 1989-2008, during the spawning run. Fig. 14 - Age distribution of walleye harvested during openwater angling fishery in the Bay of Quinte, 2008. Fig. 13 - Lamprey marking on Chinook and Coho salmon during fall, 1970-2008, in the Credit River Recreational Fishing Surveys Bay of Quinte Recreational Fishery Only the open-water fishing component of the Bay of Quinte recreational angling fishery was monitored; the icefishery was not surveyed during the winter of 2008. The 2008 open-water survey was conducted from Trenton to just east of Glenora. Angling effort was measured using on-water boat counts. Boat angler interviews provide information on catch/harvest rates and biological characteristics of the harvest. Open-water fishery Over 1,900 anglers were interviewed by field crews during the survey. Twenty-nine percent of anglers interviewed were local, 55% were from Ontario (outside the local area), 8% were from the US, and less than 8% were from elsewhere in Canada. Angling effort was targeted primarily at walleye (96%). Fishing effort was estimated to be 209,153 angler hours for all anglers and 201,669 hours for anglers targeting walleye. Numbers of walleye caught and harvested were 38,253 and 24,954 respectively. About 35% of angling effort and 40% of walleye catch/harvest occurred during May. Having declined during the late 1990s, angling Commercial Fishery Quota and Harvest Summary Lake Ontario supports a locally important commercial fish industry. The commercial harvest comes primarily from the Canadian waters of Lake Ontario east of Brighton (including the Bay of Quinte) and the St. Lawrence River (Fig. 15). Harvest statistics for 2008 were obtained from the commercial fish harvest information system (CFHIS) which is managed, in partnership, by the Ontario Commercial Fisheries Association (OCFA) and the OMNR. Commercial quota, harvest and landed value statistics for Lake Ontario and the St. Lawrence River for 2008 are shown in Fig 15 (base quota). Lake Ontario The total harvest of all species was 373,926 lb ($294,331) in 2008, down 69,774 lb (16%) from 2007. Lake whitefish Lake Whitefish harvest was 68,072 lb, 57% of base quota, and a doubling of the previous year s harvest. Fig. 15 - Map showing commercial fishing quota zones

16 Great Lakes Basin Report Special Report Yellow perch Yellow perch harvest was 112,591 lb, 25% of the base quota, and a decrease of 82,531 lb (42%) from the previous year. Over 440,000 lake trout yearlings were also stocked as part of an established, long-term rehabilitation program. Lake trout stocking is focused in eastern Lake Ontario where most of the historic spawning shoals are found. Walleye Walleye harvest was 19,288 lb, 36% of the base quota, and an increase of 4,291 lb (29%) from the previous year. St. Lawrence River The total harvest of all species was 148,963 lb ($89,954) in 2008 (Fig. 4.1.3, Table 4.1.6). Yellow perch Yellow perch harvest was 59,099 lb, 37% of base quota, an increase of 5,135 lb (10%) from the previous year. Management Activities Stocking The OMNR is committed to providing diverse fisheries (and the associated benefits) in Lake Ontario and its tributaries, based on wild and stocked fish, as appropriate. OMNR is also committed to restoration of native species and supports efforts to maintain / restore healthy, stable Lake Ontario fish communities. Rainbow trout and brown trout were stocked at various locations to provide shore and boat fishing opportunities. A portion of the rainbow trout target is stocked into streams with a potential to establish wild populations. About 80,000 Coho fall fingerlings were produced and stocked by a partner hatchery, operated by the Ontario Federation of Anglers and Hunters and supported by volunteers from the Metro East Anglers Association. Over 2.3 million young American eel were stocked into the upper St. Lawrence River and eastern Lake Ontario in an effort to restore the greatly suppressed stock. These glasseel juveniles were collected on the Atlantic coast and transported to Lake Ontario and the St. Lawrence River above the dams they face during their migration. This is part of the Ontario Power Generation Eel Action Plan and contributes to a broad, bi-national, multi-agency effort to reverse the serious decline in abundance of this globally significant species. During 2008, OMNR stocked about 1.7 million salmon and trout into Lake Ontario. Fig. 16 shows salmon and trout stocking trends in Ontario waters from 1968-2008. The New York State Department of Environmental Conservation (NYSDEC) also stocked 2.6 million salmon and trout into the lake in 2008. Over 525,000 Chinook salmon spring fingerlings were stocked at various locations to provide put-grow-and take fishing opportunities. Of these, about 25,000 were held in pens at three sites in Lake Ontario for a short period of time prior to stocking. This ongoing project is being done in partnership with local community groups. It is hoped that pen-imprinting will help improve returns of mature adults to these areas in the fall, thereby enhancing local nearshore and shore fishing opportunities. All Chinook salmon stocked in 2008 were marked with a coded wire tag and/or an adipose fin clip. This was done using Northwest Marine Technology s AutoFish, a unique, highly automated clipping and tagging system. Marking will help us determine levels of natural reproduction of Chinook salmon in Lake Ontario. The study is being done cooperatively between New York and Ontario. Anglers will begin to see marked fish in the fishery in 2009. Almost 300,000 Atlantic salmon of various life stages were released into current restoration streams: Credit River, Duffins Creek and Cobourg Brook. Fish losses as a result of power interruptions at OMNR s Normandale Fish Culture Station in 2007 and 2008 significantly affected fry and fall fingerling and spring yearling stocking rates in 2008. Atlantic salmon are produced at both OMNR and partner facilities. The Atlantic salmon broodstock is currently housed at OMNR s Harwood Fish Culture Station. Fig. 16 - Trends in salmon and trout stocking, 1968-2008 Native Species Restoration OMNR works with many partners government agencies, non-government organizations and interested individuals at local, provincial and national levels, to monitor, protect and restore the biological diversity of fish species in the Lake Ontario basin (including the lower Niagara River and the St. Lawrence River downstream to the Quebec-Ontario boarder). Native species restoration is the center piece of LOMU's efforts to restore the biodiversity. A number of fish species have been lost or persist in low numbers in the Lake Ontario basin. Twenty-two fish species formerly occurred or are currently rare in the Lake Ontario basin. Three of these species, two deepwater ciscoes, the blackfin Cisco (note that there is debate about historic existence of blackfin Cisco in Lake Ontario), and the Lake Ontario Kiyi, and blue pike (a subspecies of walleye) are thought to be extinct. Four species, Atlantic salmon, lake trout, bloater, and shortnose Cisco have been extirpated (i.e. local extinction) from the Lake Ontario basin. Four species, American eel, burbot, deepwater

Great Lakes Basin Report Special Report 17 sculpin and lake sturgeon that were once very common in the basin are now considered to be rare. The remaining species on this list were either uncommon historically or their historic status is uncertain. In addition, we acknowledge that there may be other species (small cyprinids for example) that may have been present historically but were lost prior to their documentation of their presence in the basin. The sections below describe the planning and efforts to restore lake trout, Atlantic salmon, American eel, lake sturgeon and deep-water Cisco. Success restoring these native species would be a significant milestone in improving Ontario s biodiversity. Observations of rare fish species, other than those covered in detail below, in the Lake Ontario and its tributaries during 2008 included: Burbot: 1 specimen captured in Lake Ontario off Wellington; Deepwater sculpin: 2 specimens captured in Lake Ontario off Rocky Point; Australia s Banrock Station is lead sponsor for this initiative and has committed $1.25 million over 5 years. Banrock Station is a world leader in corporate commitment to the environment, supporting conservation projects world-wide. The Lake Ontario Atlantic Salmon Restoration Program is the largest project they have supported outside of Australia. American Eel American eel are identified as an Endangered species under Ontario s Endangered Species Act. In addition, the Committee on the Status of Endangered Wildlife in Canada recommended that American eel be identified as a species of Special Concern under the Canadian Species at Risk Act. Several actions were taken by the Lake Ontario Management Unit during 2008 to address the low abundance of eel. Staff collaborated with Ontario Power Generation on the operation of the eel ladder at the Saunders Hydroelectric Dam. The number of small eel migrating upstream at the ladder, located at the Saunders Hydroelectric Dam on the St. Lawrence River, remains at a very low level. Pugnose shiner: 11 specimens were captured at 12 sites in upper St. Lawrence River; River redhorse: 16 specimens captured in the upper Bay of Quinte. Lake trout Lake trout were extirpated from Lake Ontario during the 1950s. The loss of this key predator of the offshore and valued commercial species caused both ecological and economic damage. The rehabilitation of lake trout in Lake Ontario began in the 1970s with sea lamprey control, and stocking of hatchery fish. The first joint Canada/US plan outlining the objectives and strategies for the rehabilitation efforts was formulated in 1983, with revisions in 1990 and 1997. A revision of the plan to rehabilitate lake trout in Lake Ontario is expected to be formally adopted in 2009. The current revision comes at a time when we have seen the promising signs of naturally produced lake trout, but also experienced setbacks in survival of stocked hatchery juveniles, and declining numbers of mature fish. Atlantic salmon Atlantic salmon were extirpated from Lake Ontario by the late 1800s, primarily as a result of the loss of spawning and nursery habitat in streams. They were a valued resource for aboriginal communities and early Ontario settlers, and as a top predator, they played a key ecological role in the offshore fish community. A unique partnership has been established to help bring back wild, self-sustaining populations of Atlantic salmon to Lake Ontario. This partnership, initiated in 2006, brings together the MNR and the Ontario Federation of Anglers and Hunters and a strong network of partners and sponsors. The abundance of larger yellow eel in the upper St. Lawrence River and eastern Lake Ontario remains at very low levels as was measured by three assessment programs during 2008. The average catch of American eel for 1974 to 1994 was 0.94 eels per trawl; however no eels were captured in the 300 trawls conducted between 2003 and 2008. This suggests that eels are at a very low abundance in the Bay of Quinte. Additional sampling was undertaken in Sept, 2008 in the Upper St. Lawrence River and Bay of Quinte near the stocking sites. During the fall sampling, 34 and 32 eels were caught in the St. Lawrence River and the Bay of Quinte, respectively. The eels captured from the St. Lawrence River were from eels stocked in 2006, 2007 and 2008, while the eels from the Bay of Quinte could only come from the 2008 stocking program. Other fishing capture methods (trap nets, modified trap nets) were not effective at capturing elvers or larger stocked eels. A total of 1,177 eels were released to Lac St. Pierre (1,016 captured from Lake St. Francis and 161 from USLR/LO) between May 14 and June 20, 2008. The release points were predetermined with the purpose of distributing eels throughout Lac St. Pierre based on the criteria outlined by the MRNF. During the release program, all the eels were observed to be in good health. Lake Sturgeon Lake sturgeon are a long-lived fish species, native to Lake Ontario. Their abundance in Lake Ontario declined to low levels before 1900; and a restoration plan for them is in development. In the interim, a project was conducted in 2008 to examine spawning lake sturgeon. In early June, a short gillnetting project was undertaken to determine if sturgeon were still using several historically-known spawning locations. This is the first project specifically targeting sturgeon undertaken by LOMU in recent years.

18 Great Lakes Basin Report Special Report A total of 20 sets were made in three locations, Trent River, Bay of Quinte near the mouth of the Moira River and the Napanee River. Large mesh gillnets were used, set in relatively shallow locations (average depth 3 m). To minimize mortality, gillnets were set for short durations (average set time 1 hr 49 min). The average water temperature of the netting locations was 18º C. No lake sturgeon were captured during this program. Deep-water Cisco The Lake Ontario Management Unit continued efforts to assess the feasibility of restoring deepwater ciscoes to Lake Ontario continue during 2008 through a partnership between OMNR, NYSDEC, the Great Lakes Fishery Commission (GLFC), and others. Deepwater Cisco, commonly called bloater, once dominated the deepwater fish community of Lake Ontario. Although the species is considered not at risk in Ontario because of healthy populations in Lakes Huron and Superior, it has been extirpated from Lake Ontario since the late 1950s. During 2008, plans were developed to explore experimental rearing with the target of culturing fry at the NYSDEC facility at Cape Vincent, NY, to the point they could be released into Lake Ontario. During the autumn, potential collection opportunities were explored on Lakes Huron, Superior, and Michigan. The objectives of the collection effort, planned for January 2009, were to improve the reliability of egg collection, to continue refining hatchery culture techniques and to rear a small number of fry that can be stocked into Lake Ontario. Table 8 - Summary of fishing effort, numbers of walleye caught and harvested, and walleye angling success (CUE and HUE are the numbers of walleye caught and harvested, respectively, per hour by anglers targeting walleye) during the Bay of Quinte open-water recreational fishery, 1993-2008 Table 9-2008 commercial harvest (lb) for fish harvested from Lake Ontario, St. Lawrence River, East Lake and West Lakes (two embayments)

Great Lakes Basin Report Special Report 19 Table 10-2008 commercial harvest (lb), price per lb, and landed value for fish species harvested from Lake Ontario and the St. Lawrence River, and the total for all waterbodies including East Lake and West Lakes Brown trout stocked in the Province of Ontario waters, 2008 Table 11 - Brown trout stocked in the Province of Ontario waters, 2008

20 Great Lakes Basin Report Special Report Chinook salmon stocked in the Province of Ontario waters, 2008 Table 12 - Chinook salmon stocked in the Province of Ontario waters, 2008 Coho salmon stocked in the Province of Ontario waters, 2008 Table 13 Coho salmon stocked in the Province of Ontario waters, 2008

Great Lakes Basin Report Special Report 21 Lake trout stocked in the Province of Ontario waters, 2008 Table 14 Lake trout stocked in the Province of Ontario waters, 2008 Rainbow trout stocked in the Province of Ontario waters, 2008 Table 15 Rainbow trout stocked in the Province of Ontario waters, 2008

22 Great Lakes Basin Report Special Report Lake Trout Rehabilitation in Lake Ontario, 2008 Abstract During 2008, the number of yearling lake trout stocked in May (500,908) (Fig.was at the target level of 500,000. The adjusted catch of age-2 lake trout with bottom trawls during the juvenile lake trout survey remained low and was 88% below the mean for the 1983-1989 year classes. Adult lake trout catch per unit effort from the gill net survey was 70% below the 1986-1998 average. The rate of wounding by sea lamprey on lake trout caught in gill nets was 1.47 fresh (A1) wounds per 100 lake trout and was below target for the first time in six years. Estimates from the NYSDEC fishing boat survey indicated that, for the third consecutive year, angler catch, harvest, and harvest rate of lake trout remained near record lows. The condition of adult lake trout, indexed from annual length weight regressions, increased from the reduced levels observed during 2004-2006 to a level equivalent to the high levels observed during 1996-1999. The improved condition for juvenile lake trout observed in 2006 and 2007 continued in 2008 and remained above the mean for the data series. Reproductive potential for the adult stock in 2008, determined from the annual egg deposition index, fell to a level 76% below the 1993-1998 mean. One age-2 naturally produced lake trout was collected in survey catches providing evidence of a 2006 year class, but age-1s were absent for the fourth consecutive year. Results During September 1983-2008, adult lake trout were collected with gill nets at random transects within 14 to 17 geographic areas distributed uniformly within U. S. waters of Lake Ontario. In the 16 years since the stocking cuts (1992-2007 year classes), the annual stockings were near the target level in only nine years. The USFWS Alleghany National Fish Hatchery was closed in 2005 due to an outbreak of infectious pancreatic necrosis and will remain closed for fish production through at least 2010. Lake trout for 2007 and 2008 stockings were raised at that the USFWS Pittsford and White River Hatcheries in Vermont. (Stony Point, Oswego, Sodus, Oak Orchard, and Olcott) over waters 55-m (180.4 ft) deep. Survival to age-2 The 2008 survival index, while not as low as the record low observed in 2006, was still quite low and about 88% below the average for the 1983-1989 year classes. Fig. 2 - Survival indices for age-2 lake trout stocked as yearlings, 1980 2007 Abundance of age-3 and older lake trout A total of 407 lake trout were captured in the September 2008 gill net survey (Figure 3). The CPUE of mature lake trout in 2008 (5.2) was 70% below the 1986-1998 mean and 53% below the 1999-2004 mean. The CPUE of mature lake trout in 2008 was similar to the 1983-1984 values which predated effective sea lamprey control and recruitment from the first large stockings in 1979. The CPUE for immature lake trout (generally ages 2 to 5) followed trends similar to the trawl catches of age-2 fish, but shifted ahead in time by three to four years (Figure 3). The average CPUE of immature lake trout dropped by 64% between the 1989-1993 interval (8.0) and the 1995-2004 interval (2.9). The CPUE in 2008 (2.21) was the second lowest observed and was 23% lower than the 1995-2004 mean. Fig. 1 - Total spring yearling equivalents (SYE) for lake trout strains stocked in U.S. waters for the 1972 2007 year classes Of the 500,908 yearling lake trout stocked into Lake Ontario (Fig 1), 60% were Seneca Lake wild (SEN) and 40% Lake Superior (from Traverse Island broodstock). All fish were stocked from a landing craft, offshore at five sites Fig 3 - Abundance of mature and immature Lake trout calculated from catches made with gill nets during September 1983-2008 From 1992 until 2004, the CPUE exceeded the target, but fell below target during 2005 to 2008, coincident with the decline of the entire adult population.