Survey of the Fish Populations of the Lower Cosumnes River. Amy Harris

Transcription

1 Survey of the Fish Populations of the Lower Cosumnes River Amy Harris Spring,

2 I. Introduction The information that is available on the fish communities of the Cosumnes river consists primarily of salmon data collected during the past 20 years. Such surveys were usually conducted in the late spring or summer (Department of Fish and Game, Region 2 Headquarters, Cosumnes files). There is very little information available on other species of fish or any collected during the winter and spring. In these seasons, flooded habitats such as sloughs and backwaters provide important nursery habitat and refuge from the fast current of the main river for many juvenile fish. Surveys were conducted in the spring of 1996 to identify the fish present in the lower Cosumnes River. The objectives of the study were to document the occurrance of native species in the river, and to estimate the effectiveness of the technique and sampling design for future studies. Several native fish were found, including the Sacramento splittail, a "Species of Special Concern" in California. II. History of the Cosumnes River Fisheries Prior to European settlement, the Cosumnes River and its fishery resources were used by Native Americans living along the River floodplain. The gold rush brought the first major changes to the River in During the 1850 s, hydraulic mining, water power, and several diversions changed the natural regime of the River. Farming and cattle ranching became the primary economic uses of the area in the late 1800 s, and water diversions drew heavily on the River to support these operations (Miller, 1986). While no records were found of the chinook salmon run in the Cosumnes River prior to 2

3 the 1950 s, there are detailed accounts of the regions's salmon fisheries. Salmon became an important food item during the gold rush and railroad building of the 1850 s. By 1883, 21 canneries were established in California, and most of these were located in the Bay Area. Gill netting, fyke netting, and seining were used for fishing up until Habitat destruction in the form of mining, logging, and irrigation diversion also depressed salmon populations, particularly those found in the American, Feather, and Yuba Rivers. In addition, ocean trolling was increasing from However, the greatest blow to the runs was the construction of major dams beginning in the 1940's, which blocked natural migration routes and prevented returning adults from utilizing much of their natural spawning range (Reynolds and Reavis 1990). Although laws and other measures were enacted to protect the fisheries, the decline of the Valley's great salmon runs had already begun. The U.S. Fish Commission began to stock the Sacramento River, and by 1883 the Commission was advocating the use of fish screens on all water diversions. The State legislature terminated commercial canneries in 1920 and the use of gill nets in 1957 (Reynolds and Reavis, 1990). Salmon spawning gravels were evaluated in the Cosumnes River in the 1950 s by the California Department of Fish and Game. Data recorded included the percent composition of large, medium, small, or fine gravels, and the velocity and depth of the stream. Line transects were used, and the stream was given a rating as to the percentage of usable gravel. The Cosumnes River was found to have high potential as a salmon spawning stream, with a large area of good quality gravel from Sloughhouse (Meiss Road) to Latrobe Road (see Figure 1). The section of the Cosumnes River with the best spawning gravels also had extensive stretches of willow and cottonwood corridors, which provided bank stabilization and prevented 3

4 rapid warming of the river. The reaches without riparian corridors were subject to warming trends and siltation problems. These siltation problems were also a result of past hydraulic mining and cattle grazing along the banks of the river (Department of Fish and Game, Region 2 Headquarters, Cosumnes files). Figure 1: Spawning gravel locations in the Cosumnes River Annual spawning run estimates for chinook salmon have been made in the Cosumnes River for most of the past 40 years, and were based primarily on carcass counts of adult return spawners (see Appendix I). These surveys suggest that during this period, runs ranged between a low of zero and a high of 5000 individuals. However, with sufficient flows and otherwise good habitat available, it has been estimated that the Cosumnes could support a run of over 17,000 chinook salmon (Miller, 1986). In addition to annual spawning run estimates, the Department conducted surveys for redds. Often, redds (nest depressions in gravel) are surveyed along with carcass counts to 4

5 estimate the annual spawning run. A 1984 aerial survey listed redds as "too numerous to count" in the area of Highway 16 to within two miles of Dillard Road. A similar flight in 1983 found no redds. A 1982 flight found 23 redds (9 upstream of Highway 16, 14 downstream of Highway 16 (Department of Fish and Game, Region 2 Headquarters, Cosumnes files). This indicates that salmon were using the same area of spawning gravels in the early 1980 s that was identified as good spawning gravel in the 1960 s. Both the redd counts and carcass counts that have been taken in the past were limited by the water condition of the river at the time of the survey. Because these surveys only lasted for one or two days during the fall season, water depth and visibility may have prevented detection of redds, redds could have been washed out by heavy storms, or adult salmon might not have been able to migrate upstream that year. Error!Water flow is one of the most limiting factors affecting the fish of the Cosumnes River, and salmon in particular. Adult salmon must have enough water in the fall to migrate upstream to spawn, and the juveniles must have good conditions in the spring to migrate out of the river. Some historical flow records are available as far back as the beginning of this century. However, it is probable that agricultural diversions were already occurring by this time (Department of Fish and Game, Region 2 Headquarters, Cosumnes files). A study of juvenile salmon in 1964 and 1965 in the Cosumnes River attempted to estimate the flows needed for successful outmigration. What they learned was that the time of migration varied according to the level of flows that year. In a low-flow or drought year, outmigration might be delayed, which suggests that the fish are adapted to variable conditions in the river. Later outmigration could potentially subject the juveniles to higher water temperatures and more irrigation diversions. Adult salmon and steelhead are also dependent on water in the fall when 5

6 migrating upstream to spawn. Water diversions at this time can affect the spawning success of these fish (Department of Fish and Game, Region 2 Headquarters, Cosumnes files). It is significant to note that many illegal dirt and gravel dams have been constructed along the river for agricultural diversions. An aerial flight in 1972 counted ten dirt dams and three gravel dams between Rancho Murietta and Highway 99 (Department of Fish and Game, Region 2 Headquarters, Cosumnes files). Many such dams have probably been built annually during most of this century. These diversions both reduce the amount of water flowing down the river, and catch small fish in the intake pipes. Another factor affecting the salmon runs in the Cosumnes is the introduction of hatcheryreared juveniles. Surplus chinook fry from the Nimbus hatchery on the American River have been planted in the Cosumnes River periodically since 1980 (see Appendix II). This may have had an effect on the wild stocks of Cosumnes chinook salmon. Although there is little or no data on the subject, the genetic quality of returning adults may have been compromised through interbreeding with hatchery fish and swamping the gene pool. Most of the historical data available on fish of the Cosumnes has been related to the run of fall-run chinook salmon. However, a number of additional surveys have provided some insight on other species. In 1973 and 1974, Mark Caywood conducted surveys for a Master s thesis at California State University, Sacramento. He surveyed two dead-end sloughs north of the mouth of the Cosumnes (0.5 and 1.5 km above the confluence). He found many of the same species that were found in our 1996 survey, with a few exceptions. Caywood found warmouth bass, redeye bass, and green sunfish, none of which were found in the 1996 survey. He also found 6 delta smelt (April 1974), but because this is the only account of delta smelt in the Cosumnes and no 6

7 voucher specimen was kept, there is some question about the validity of this record (Caywood, 1974; Department of Fish and Game, Region 2 Headquarters, Cosumnes files). A 1994 survey of the Cosumnes river by the Department of Fish and Game found similar species to the present 1996 survey. Brown trout, rainbow trout, and California roach were found in 1994 in the upper forks of the Cosumnes, which are areas not surveyed in Green sunfish, speckled dace, and steelhead smolts were also found in the lower and middle reaches of the Cosumnes in the 1994 survey. These differences may be due to differences in sampling methods (i.e., Fish and Game electroshocking versus netting), time of the year of sampling (i.e., May through September versus March through June), or variation in water levels in the river in 1994 and III survey of the lower and middle Cosumnes River Methods. Six sites were sampled approximately once per week from March 24, 1996 through June 16, 1996 (see figure 2). The survey extended from near the mouth of the Cosumnes upstream to Rancho Murietta, with most of the sites concentrated in the lower reaches. A beach seine net, 6 feet deep, 35 feet long, with 1/4 inch mesh, was swept along the bank of the stream. Depth was from 2 to 5 feet deep, and the average seine distance was approximately 75 feet. The seine corraled the fish into a bag at the back of the net, and when the net was brought to the shore, the fish were removed and transferred to a basket. The number of each species and the length (in millimeters, standard length) of each individual specimen was recorded, and the fish were then released, except for a few individuals kept as vouchers. (Voucher specimens are preserved and stored at California State University, Sacramento). On June 13, six fyke nets and 7

8 two large-mesh gill nets were set overnight in Tihuechemne Slough to compare results with the seine net. (Fyke nets are similar to traps, constructed of panels of netting; they differ from the seine net in that fish swim into them and cannot escape, whereas the seine net actively corrals the fish. A gill net is a straight panel of netting which physically entangles fish that swim into it. Because this often kills the fish, we used a large size mesh to avoid capturing smaller fish, including the Sacramento splittail, and to reduce the number of fish killed). These nets provided a good comparison, because the seine is small enough that it is probably less effective at capturing the large fish, while the gill net used was selecting for large fish. locations of the 1996 spring survey of the fish of the Cosumnes River Results. The seine net yielded more species and numbers of fish, and the only different species found with the gill net was a striped bass. The species caught, minimum size and maximum size, site sampled, and dates are listed in the appendix. The native species caught were: blackfish, chinook salmon, hitch, lamprey (probably Pacific), Sacramento splittail, Sacramento squawfish, Sacramento sucker, prickly sculpin and tuleperch. The introduced species caught were: American shad, bass (smallmouth, largemouth, and spotted), sunfishes (bluegill, redear, and hybrid), bullhead (black, yellow, and brown), carp, catfish (white and channel), crappie (black and white), goldfish, inland silverside, logperch, mosquitofish, striped bass, threadfin shad, and shiners. The only red shiners were caught at the Oneto property, and the rest appear to be golden shiners. This was the first time in several years 8

9 that Sacramento splittail have been recorded in the River, and they were found at three locations during May and June. Table 1: Summary of fish species identified in the 1996 survey of fish populations Common Name* Scientific Name Total Number Caught American shad Alosa sapidissima 3 smallmouth bass Micropterus dolomieui 27 blackfish Orthodon microlepidotus 22 bluegill Lepomis microlophus 96 bullhead Ictalurus spp. 73 carp Cyprinus carpio 53 channel catfish Ictalurus punctatus 15 catfish (white) Ictalurus catus 1 chinook salmon Oncorhynchus tshawytscha 68 crappie Pomoxis spp. 172 goldfish Carassius spp. 63 hitch Lavinia exilicauda 86 inland silverside Menidia beryllina 107 Error!lamprey Lampetra sp. 6 Error!largemouth bass Micropterus salmoides 4 Error!logperch Percina caprodes 76 Error!mosquitofish Gambusia affinis 47 Error!redear sunfish Lepomis microlophus 43 9 Error!sculpin Cottus sp. 36 Error!shiner Notemigonus sp. 300 Error!Sacramento splittail Pogonichthys macrolepidotus 35 Error!spotted bass Micropterus punctulatus 10 Error!Sacramento squawfish Ptychocheilus grandis 43 striped bass Morone saxatilis 1

10 Discussion. The identity of the juvenile chinook salmon caught presented quite a mystery, and suggested several interesting explanations. It was believed that the adult Cosumnes chinook never made it into the river to spawn in the fall of 1995, because the rain came so late. A carcass count found no adults. However, the Department of Fish and Game planted approximately 200,000 fry from the Nimbus hatchery in January. Although this confounded our survey of Cosumnes chinook salmon, it did provide an interesting insight into the habitat conditions of the river for juvenile salmon. The juvenile salmon we caught were much bigger than we expected and appeared healthy. No fin clips or other markings were observed, and most individuals had developed some degree of smolt coloration (silvery). Their size placed them into spring-run category, which is inconsistent with the prevailing view that the only salmon spawning run in the Cosumnes is a fall run. These juveniles could have migrated from the delta via the Mokelumne up into the Cosumnes to use the nursery habitat, but there are no known spring-run salmon populations nearby. The most likely explanation is that the fish caught in our seine were the hatchery fish planted in January, but were able to grow faster than typical juvenile fall-run salmon. This would suggest that the Cosumnes has favorable nursery habitat that allows fish to grow at a relatively faster rate than normal. It also suggests that such juveniles would tend to enjoy higher survival rates upon outmigration. The flooded areas along the Cosumnes probably provide warmer, more productive feeding areas out of the main current of the river. Further studies could provide more definitive results on this subject. Some of the smaller fish sampled were difficult to identify and may be the source of a minor amount of inaccuracy in our results. For example, many of the small cyprinids with a black spot at the base of the tail were recorded as 10

11 hitch. It is quite possible that many of them were juvenile blackfish, but it is difficult to distinguish the two species until later in the season when the juveniles are larger. (Both adult blackfish and adult hitch were captured during the study.) In addition, some of the bass were recorded as spotted bass, which is also a species that is difficult to distinguish from other bass in their juvenile form. Voucher specimens were kept of most species caught. There has historically been a steelhead run in the Cosumnes (Department of Fish and Game, Region 2 Headquarters, Cosumnes files), so it is possible that juvenile steelhead were not captured this spring because the adults were not able to migrate upstream last fall because of the lack of rain in November and early December. As with any survey, there were limiting factors that affected the results. Sampling was planned to begin in February but, because of the time it took to obtain collecting permits, field work did not begin until late March. Water levels varied considerably during the survey period, affecting when and where we were able to seine. Physical conditions in general are variable in the river, and this led to an uneven location of sampling points. Given such factors, sampling conducted in different seasons and in different years will yield a more complete picture of the use patterns of the river by the different fish species. Our survey has increased our knowledge of the fish populations in the Cosumnes River, but it should not be considered definitive. Recommendations. There is good potential for protection and restoration of the fish populations of the Cosumnes River. Many of the native species are still present, and further studies could establish if their populations are stable and which habitats are most critical. Therefore, the following recommendations are proffered: 11

12 1. The Conservancy should request that the California Department of Fish and Game stop stocking hatchery-raised salmon in the Cosumnes River. Based on the resiliency of salmon runs before the construction of most of the local dams (Miller, 1986), the salmon in the Cosumnes should be able to increase their numbers without the stocking of hatchery fish. The limiting factor for salmon in the past has been water; high enough flows in the fall and spring for migration (Department of Fish and Game, Region 2 Headquarters, Cosumnes Files). Stocking American River fish in the Cosumnes will not address the issue of water in the river, and is unlikely to be effective in the long term. 2. All diversions along the river should be screened, and illegal diversions should be identified and removed. This is most likely an enforcement issue for Fish and Game. 3. Seining surveys for outmigrant steelhead and salmon juveniles should be continued in the winter and spring seasons to assess their populations and to determine growth rates. If the juveniles are found to have significantly higher growth rates than juveniles of other rivers, this will reflect very favorably on the rearing conditions of the Cosumnes for juvenile salmon and as a high-return-on-investment site for habitat restoration. nd steelhead should be conducted in the fall. Spawning gravel conditions can be assessed in early fall, and carcass and redd counts can be made in November and December. This will produce a more complete picture of the population status of lower Cosumnes salmonids. 5. Now that Sacramento splittail have been documented to be spawning in the Cosumnes River, population sampling for this species should be conducted at least monthly. This would provide data on growth rates of juveniles, and information about when and how they are using the sloughs. Expansion of methods used might give us more information on the adult 12

13 splittail. 6. Overall sampling design should be modified. Sampling once or twice a month,as opposed to once per week, would be sufficient. Seining was effective, but it would be useful to continue including other methods, such as the gill nets and fyke nets. In May, we switched from 1/8 inch mesh to 1/4 inch mesh on the seine net, which greatly reduced the impact to juvenile fish, and improved our efficiency. I would not recommend using a net with smaller than 1/4 inch mesh. To sample the larval fish, other methods could be used. 7. Water temperature data should be recorded while fish sampling. This data could be very useful in producing accurate temperature profiles of the river and serve as a measure of habitat quality. (This information, along with flow records from DWR, could be included in the hydrologic model at Cosumnes River Preserve). 8. The installation of fish screens on all pumps at the Cosumnes River Preserve should be made a high priority. Most of the native fish of the River, some of them threatened or declining, are represented in this reach of the Cosumnes. Unscreened diversions can have major impacts on fish populations. Conclusions Based on this preliminary study, the fishes of the Cosumnes River appear to be in good physical condition due to, among other things, the lack of major impoundments, high quality habitat and the natural flooding regime. The Cosumnes provides a diversity of habitats unavailable in most rivers in the area. A high diversity of fish is present, including many native fish. More study will be needed to establish an accurate measure of the current ecological health 13

14 of the River's fishes, and this study should provide a good starting point. Error! 14