Pine River Instream Fish Habitat Assessment

Pine River A report on the Pine River s instream fisheries habitat 1 Pine River Instream Fish Habitat Assessment Michigan Trout Unlimited February 2015 Kristin Thomas Dr. Bryan Burroughs

2 Table of Contents INTRODUCTION... 4 Table 1. Michigan stream and river temperature classification criteria... 4 Figure 1. Map of the Pine River.... 5 DATA EXAMPLES... 5 Figure 2. Hypothetical bedform composition data for a healthy balanced river.... 7 Figure 3. Hypothetical substrate composition data for a healthy river.... 8 Figure 4. Hypothetical in-stream habitat data for a river with good diverse habitat... 9 METHODS... 10 Table 2. Bedform delineation... 11 Table 3. Substrate classes used to denote substrate composition.... 11 Table 4. Descriptions of the 18 Pine River sites.... 12 Figure 5. Pine River Substrate Composition... 12 Table 5. Description of the six Pine River segments used for analysis... 14 RESULTS AND DISCUSSION... 15 PINE RIVER ANALYSIS: WHOLE RIVER... 15 Figure 9. Pine River bedform delineation, bottom substrate, and in-stream fish cover.... 17 PINE RIVER ANALYSIS: BY SEGMENT... 21 Bedform Structure... 21 Figure11. Pine River bedform diversity.... 22 In-stream Habitat Availability... 22 Figure12. In-stream habitat structure in the Pine River.... 23 Substrate Composition... 23 Recommendations and Management Actions... 24 LITERATURE CITED... 29 APPENDIX 1.... 30

3 Purpose & Context Many coldwater streams in Michigan, including the Pine River, lack comprehensive data on in-stream fish habitat conditions. Research has been done to verify that temperature, catchment size, and 90% exceedance flow have a substantial impact on fish community (Zorn et al. 2009, Zorn and Wiley 2004). However, at this time there is not research available which relates the amount, quality, or spatial distribution of in-stream habitat to fisheries population dynamics (density or size structure). Some work has been done to determine if the addition of woody debris has positive impacts on fisheries populations (Roni and Quinn 2001, Bryant 1983), but has not looked at how much wood is needed or optimal. It is our long-term intent to develop paired habitat and fisheries data sets that can be used to statistically determine the degree to which in-stream habitat, substrate, and bedforms shape fisheries populations in Michigan. The ultimate goal of having that scientific insight would be to assess a stream and fishery and be able to confidently diagnose its limiting factors and ensure that actions taken to improve fisheries will result in those benefits being realized. With that in mind, fisheries habitat data was collected, summarized, and discussed in the context of prioritizing restoration and protection efforts in the Pine River. An emphasis was placed on coldwater fisheries habitat. Habitat mapping was used because it provides a comprehensive habitat inventory for the entire river, or a segment of river, in contrast to a small random subsample that may not accurately depict the variability of habitats that truly represent a river s current conditions. The Pine River was surveyed from 20 Mile Rd. (North Branch Pine River) to the Tippy Reservoir for a total of 55 miles, from 2011-2014. This report summarizes the data collected during this survey. It is important to note, that currently, rigorous statistical relationships between instream fish habitats and fish populations are not available. This means that we are not able yet, to place these results for the Pine River, in a broader statistical context for identifying and justifying priority improvements to target. At this point in time, we must interpret these results in limited context with the other rivers we have surveyed, and use the professional or expert judgment of those intimately familiar with our streams geomorphology and fish populations, and with experience in the practice of stream enhancement techniques and costs. With that said, this report provides summaries of the results of the survey, and interpretations and recommendations that represent TU professional staff s best judgment. This report will be best put to use through engaging with other partners and practitioners in review and interpretation, to ensure we all work together to improve and protect the Pine River. If you review this report and would like to provide comments, alternate interpretations, or recommendations for improving future versions, we welcome your ideas and participation.

4 Introduction The Pine River is a high quality trout stream located in northwest Michigan. The mainstem of the Pine is approximately 49 miles long, draining 265 square miles. The Pine River is located in the Manistee River watershed. The entire mainstem of the Pine River is considered a cold small river by the State of Michigan (Table 1). Table 1. Michigan stream and river temperature classification criteria. Temperature ranges are based on predicted mean July water temperature ( F). These classifications are the base for protection limits from large quantity water withdrawals under MI statute (Part 327). Classification Temperature Range Cold <63.5 F Cold-Transitional 63.5-67.1 F Cool 67.1-69.8 F Warm >69.8 F Prior to this survey there was limited current fish habitat data available for the Pine River. Road stream crossing and bank erosion inventories are available from Conservation Resource Alliance and the DNR has habitat data for a few select sites. These are great tools; however, they don t allow focus on the status of in-stream fish habitat conditions in the entire river. The purpose of this survey was to catalog in-stream habitat to determine how it may be limiting the coldwater fishery. It is important to note that fish habitat data is only one of the tools used to identify factors that may be limiting a coldwater fishery, albeit a critical one in which data is typically lacking. Habitat mapping differs from many types of habitat monitoring in that fish habitat is surveyed in the entire river, or an entire sub-section of a watershed. It serves as more of a census than a survey. It included; delineating the river channel into bedform types (run, riffle, or pool), recording the length, location, and width of each bedform unit; and the characterization of the amounts of in-stream fish cover (aquatic vegetation, woody debris, and deep water) and streambed substrate composition in each bedform unit. The full methodology is explained and supported in a separate manual, found at, http://www.michigantu.org/index.php/river-stewards-manual/habitat-mapping. Each of these variables is important to the health of a coldwater fish community. A variety of bedform structures are needed for a healthy fishery. Each species of fish, at different stages of their life, have specific needs for survival, growth and feeding, and reproduction, and it takes a variety of habitats to provide for all of those unique needs. For example, riffles with coarse substrate are used for spawning and are critical habitat for numerous species of macroinvertebrates, which provide food for trout. Bottom substrate heterogeneity is also important in providing a variety of food sources. A variety of substrate types (gravel, cobble, silt, wood, leaf packs, etc.) provide habitat for a diverse macroinvertebrate community and thus a variety of food sources for coldwater fish. Areas that can hold and hide fish are also important. Woody debris, deep water, and aquatic vegetation are examples of fish habitats which provide cover. Trout and other fish can seek refuge from predators in these areas.

5 From 2011 through 2014, approximately 55 miles of the Pine River were mapped (Figure 1). Habitat mapping data collected on the Pine River is summarized in this report. Trends in bedform composition, substrate composition, and fish habitat structure were compared in six segments of the Pine River. End Start Figure 1. Map of the Pine River. Mapping was completed from the start point to the end point. Data Examples As discussed in the Purpose & Context section, we do not currently possess well-developed quantitative relationships between instream fish habitat variables and stream fish populations. However, we do have confidence in several general ecological principles. 1.) Habitat heterogeneity and diversity is desired. It provides for habitats to suit many macroinvertebrate and fish species and their various life stages, generally leading to healthy populations, diverse fish communities, and ecosystem resiliency. In contrast, homogeneity of habitats, while possibly benefiting a few select species, generally leads to less productive and resilient fish communities. 2.) Stream fish such as trout, unless prevented from migrating throughout a river system by impassable barriers, will move considerable distances to reach unique habitats they need for different purposes. If connectivity between river segments exist, each segment need not offer all habitat elements in ideal levels, rivers can form mosaics of different habitats that taken and functioning as a whole provide all the necessary elements. 3.) Trout, salmon and steelhead are lithophilic spawners, meaning they require gravel substrates of the right size ranges, with specific water velocities to reproduce. We do not well understand the exact amounts of this habitat in a stream that are required to ensure maximum spawning potential and success for a given population, but these habitats are essential.

6 4.) Wood material is critically important in Michigan streams, for influencing channel form, localized substrates, nutrient cycling, substrates for macroinvertebrates, and cover for fish. We do not yet understand how much wood is optimal. Is more wood always better for trout, or is it only better to a certain point, with no real benefit after that? We do not yet understand finetuned wood dynamics, but do know it is a critical component to healthy stream fisheries in the Midwest. 5.) Deep water, defined here as >2.5 ft. deep, provides security and comfort to many species of fish in streams, and for large sizes of trout. Very wide and shallow habitats can be productive habitat for small fish and juvenile trout, but generally, larger sizes of stream trout require presence of deep water and other forms of cover. 6.) Moderate slopes or gradients of streams tend to lead to the formation of more riffle and pool bedforms, interspersed with runs. As slopes decrease, riffle and pools become less frequent, and bedforms are dominated by runs. When run bedforms are dominant, it becomes essential that habitat complexity and diversity is accomplished by other habitat elements such as deep water, wood material, and aquatic vegetation. 7.) We are not yet able to confidently state how much sand substrate is deleterious to a trout population. The negative impact of sand to a trout population generally, has been well documented. But exact impacts to a population will be dependent on many other variables, including the abundance and distribution of other forms of critical habitat (which may or may not co-vary with sand). So, we examine the results of instream fish habitat assessments through these very general principles, looking first for clear and obvious deficiencies or imbalances of critical habitats, and secondarily for potential elements that could be optimized further in specific locations. The following are hypothetical data scenarios to familiarize the reader with these concepts and the data summaries to follow.

Percent Total River Area Pine River A report on Pine River Instream fisheries habitat 7 A healthy stream will have diverse bedform structure with ample run, riffle, and pool habitat. The river will not be dominated by one bedform type (Figure 2). River A has a good balance of bedform types, whereas River B is dominated by run habitat with little riffle or pool habitat available. The dominance of run habitat in river B may indicate a problem. A) 80 70 60 50 40 30 20 10 0 Pool Riffle Run B) Figure 2. Hypothetical bedform composition data for a healthy balanced river (A) and a river with limited bedform heterogeneity (B).

8 A variety of substrate types are also present in a healthy river. It is especially important that fine sediments (sand and silt) do not dominate a river bottom. Erosion is a major source of pollution to our waterways, an overabundance of fine sediment may be a sign that there is an erosion problem in the watershed, or a legacy of past sedimentation that has not been flushed out of the system. A healthy river will have a balance of substrate types (Figure 3). River A has a good balance of fine and hard substrate; whereas river B is dominated by silt and sand with little hard substrate present. A) B) Figure 3. Hypothetical substrate composition data for a healthy river (A), and a river with excess fine sediment (B).

9 In-stream habitat diversity, or fish cover is also an important portion of what makes a stream ideal for coldwater fish. Fish need a variety of places to seek cover from predators including aquatic vegetation, woody debris, and deep water. River A has abundant, diverse in-stream fish habitat (80%); whereas, river B has sparse in-stream habitat available (25%) (Figure 4). A) B) Figure 4. Hypothetical in-stream habitat data for a river with good diverse habitat (A), and a river deficient in-stream habitat (B). Graph A in Figures 2-4 depict a healthy river, ideally each river mapped will have data similar to that generally seen in the A graphs. Graph B in Figures 2-4 depict issues which may be indicative of a limitation to the coldwater fishery. When we see data similar to that in the B graphs restoration or enhancement may be needed, and more in-depth analysis and discussion is appropriate.

10 Methods Methodological details for this instream fish habitat assessment can be found in full detail in report form, at: http://www.michigantu.org/index.php/river-stewards-manual/habitat-mapping. This survey was conducted by volunteer members of the Pine River Chapter of Trout Unlimited, with support from interns or staff at Michigan Trout Unlimited. Members were trained in habitat mapping methods by Michigan Trout Unlimited Aquatic Ecologist Kristin Thomas. All mapping was completed during average or low flow conditions. It is important that habitat is not mapped during times of high flow because high flow can make it difficult to distinguish bedform delineations. Training included instruction on how to determine bedform delineation, substrate classification, and practice visually estimating percent of streambed. Stream diagrams were used to practice estimating the percent of streambed occupied by substrate types and fish cover. Volunteers estimated substrate composition and fish cover for each diagram. A key with a grid and actual percentages were then provided. This exercise was used to help volunteers visually estimate percent of stream bottom. Bedform delineation and qualitative observations were derived through independent visual observations and evaluations. Bedform delineation involved the categorization of the stream into bedforms (run, riffle, pool, rapid, as defined in Table 2). The length and widths (top and bottom) of each bedform section were measured. Latitude and longitudes were recorded at the top and bottom of each bedform section using a handheld GPS. Measurements of bedform lengths and widths were made with a Nikon Laser Rangefinder (+/- 0.5 yard accuracy) or a tape measure. Quantitative streambed substrate composition measurements were made through visual estimation. The percent area of each bedform segment occupied by clay, silt, sand, gravel, cobble, or boulder was estimated visually. Substrate classification followed Wolman size classes for sand, gravel (all sizes combined), and cobble (all sizes combined) (Table 3). The percent area of streambed in each bedform section covered by woody debris, aquatic vegetation and deep water (>2.5 ft.) was also visually estimated. The amount of wood, vegetation, and deep water was expressed as a percent of streambed area (5% increments). The maximum depth present in each bedform section was also recorded. In cases were maximum depth could not be measured; maximum depth was listed as greater than 4 feet.

11 Table 2. Bedform delineation explanation. Bedform Description Run Riffle Fast or slow current, unbroken water, average depth. Swift current, turbulent broken water, shallower than average depth. Pool Slow or no current, unbroken water. Generally about 1.5 times deeper than average depth. Rapid Waterfall Swift current, very turbulent, broken water. Large boulders or bedrock often breaking the surface. The majority of the stream flow over a ledge or cliff. Table 3. Substrate classes used to denote substrate composition. Particle Description Clay Silt Sand Gravel Cobble Boulder Bedrock Very fine sticky texture. Easily forms ribbons when rolled in hand, generally reddish or gray in color. Very fine texture. Smooth, silky feel when handled. Crumbles readily when handled. Single sand grains are apparent. Rocks 1/16 to 2 ½ inches in diameter Rocks 2 ½ to 10 inches in diameter. Rocks greater than 10 inches in diameter. Solid rock surface, not the tops of boulders. The Pine River was originally divided into 18 habitat mapping sites, for the purpose of organizing field data collection (Table 4). In most cases, access points dictated the beginning and end of each site. Habitat data for all of the mapped portions of the river were analyzed and then the 18 sites were grouped into 6 analysis segments. Segments were chosen based on commonalities in habitat conditions, and clear contrasts between them (Table 5). Figures 5-7 below are provided, to illustrate that the consolidation into 6 segments for analysis was based off similarities in in-stream habitat elements, and not arbitrary grouping that would obscure significant differences between the segments.

12 Table 4. Descriptions of the 18 Pine River sites. Site Name Site Description Segment Pine 1 20 Mile to End of 230 th Segment 1 Pine 2 End of 230 th to 17 Mile Segment 1 Pine 3 17 Mile to Raymond Rd. Segment 1 Pine 4 Raymond Rd. to Briar Patch (5 Rd.) Segment 1 Pine 5 Briar Patch (5 Rd.) to 6 Mile Segment 2 Pine 6 6 Mile to Coe Creek Segment 2 Pine 7 Coe Creek to Skookum Road Segment 2 Pine 8 Skookum Road to N. Pine River Road Segment 2 Pine 9 N. Pine River Road to State Road Segment 3 Pine 10 State Road to Silver Creek Campground Segment 3 Pine 11 Silver Creek Campground to Lincoln Bridge Segment 3 Pine 12 Lincoln Bridge to Elm Flats Segment 3 Pine 13 Elm Flats to Poplar Creek Segment 4 Pine 14 Poplar Creek to Dobson Bridge Segment 4 Pine 15 Dobson Bridge to Peterson Bridge Segment 4 Pine 16 Peterson Bridge to Forest Rd. 7319 Segment 5 Pine 17 Forest Rd. 7319 to Stronach Dam Road Segment 5 Pine 18 Stronach Dam Road to Tippy Pond Segment 6 Figure 5. Pine River Substrate Composition. Fine clay, silt, and sand. Hard gravel, cobble, and boulder. For the 18 original sites (vertical red lines depict segments).

13 Figure 6. Pine River bedform structure, in the 18 original sites. Figure 7. Pine River fish cover, in the 18 original sites.

14 Table 5. Description of the six Pine River segments used for analysis. Numbered in upstream to downstream order (from East to West approximately). Segment Name Segment Description Segment Length (miles) Segment 1 20 Mile to Briar Patch (5 Rd.) 12.45 Segment 2 Briar Patch (5 Rd.) to N. Pine River Road 5.68 Segment 3 N. Pine River Road to Elm Flats 4.86 Segment 4 Elm Flats to Peterson Bridge 14.30 Segment 5 Peterson Bridge to Stronach Dam Road 8.84 Segment 6 Stronach Dam Road to Tippy Pond 2.27 6 5 4 3 2 1 Figure 8. Map of the mainstem of the Pine River, showing the 6 main segments of the river related to distinct differences in instream fish habitat conditions. Boundary descriptions found in Table 5. Habitat features for each section were summarized (Table 6). For all analyses, percent of total streambed was used. For example, to determine what percent of the river is run, riffle, and pool the total area of run, riffle, and pool was calculated and then expressed as a percent of total streambed area. To calculate the area of each bedform section the mean bedform section width (top width + bottom width/2) was multiplied by bedform section length. Percent substrate and habitat was calculated by expressing the percent substrate or habitat as an area (i.e. (percent gravel/100)*bedform section area). The total area of sand, gravel, cobble etc. was then summed and expressed as a percent of total stream or segment area. Thus, each percent presented on a graph represents the proportion of total stream bed occupied by that in-stream habitat element as estimated for this study. The deepest point in each bedform section was also recorded.

15 Results and Discussion Table 6. Instream fish habitat summary data for the Pine River. Percentages and proportions are percent are of the described section. All Sections Section 1 Section 2 Section 3 Section 4 Section 5 Section 6 Mapped Total Length (ft.) 289,671 65,716 29,981 59,842 75,482 46,656 11,994 Width (ft.) Mean 50 36 47 47 54 60 142 Range 15-537 15-85 30-93 26-75 28-102 36-108 45-537 Percent Run Bedform Percent Riffle Bedform Percent Pool Bedform 75 19 6 89 7 3 % Deep Water (>2.5 ft.) 33 33 41 28 44 34 9 % Woody Debris 9 17 10 7 8 6 6 % Aquatic Vegetation 6 12 5 8 5 2 5 Total Section - % Clay 9 5 3.5 10 14 11 0.5 Total Section - % Silt 4 11 3.5 4 2 1 4 Total Section - % Sand 44 47 32 33 43 28 92 Total Section - % Gravel 24 12 23 29 28 37 3 Total Section - % Cobble 14 19 28 19 8 16 0.25 Total Section -% Boulder 5 6 10 5 5 7 0.25 58 23 19 70 24 6 75 20 5 59 35 6 100 0 0 Pine River Analysis: Whole River The Pine River mainstem, as a whole, has 75% run habitat, 19% riffle, and 6% pool bedforms (Figure 9). While it is dominated numerically by run habitat, 75% run bedforms is relatively low in comparison to other Northern MI trout streams we have surveyed to date (Figure 10-A). The 19% riffle bedforms, along with the relatively large amounts of gravel and cobble substrates it provides, does not seem to indicate that the river is limited by hard substrates or riffle areas. Likewise, the 6% pool bedforms is moderate, and combined with total area of deep water (>2.5 ft.) at 33%, does not indicate that the Pine River is lacking in deeper water habitats. So the 74% run bedform estimate should be viewed, in regional context, as not excessive, and probably well-balanced for streams in this region. Similarly, substrate composition in the Pine River was relatively balanced (Figure 9B). Sand did still comprise the dominate substrate type at 44%. But, gravel (24%) and cobble (14%) substrates were abundant. Gravel substrates were moderate compared to other regional trout streams (Figure 10-B). It appears that despite the high average slope of the river, which would lead to the expectation of higher percent gravel, that those high slopes and flows of the Pine result in relatively high proportions of cobble and boulder substrates, and gravel abundance is relatively moderate. The Pine River has the highest abundance of boulders seen on any river yet surveyed. Conversely, it along with the Sturgeon River (commonly cited as the two highest gradient rivers in the Lower Peninsula) had the lowest relative abundances of silt substrates. When substrate types are grouped into hard or fine groupings, based on

16 their ecological function (fine = sand & silt), the Pine River is illustrated as having a relatively high abundance of hard substrates, compared to other regional streams that have been surveyed (Figure 10- C). The percent area of the streambed occupied cumulatively by wood debris, aquatic vegetation, and deep water, referred to here as cumulative fish cover, was nearly 50% of the stream bed area. When compared to other regional trout streams, this level of fish cover ranks as moderate low (Figure 10-D). Deep water area was high at 33%, a unique and valuable asset to fish habitat (Figure 10-E). Wood debris was low at 9%, in fact, the lowest seen of any of the rivers we ve surveyed to date (Figure 10-F). Aquatic vegetation, at 6%, was also low relative to other rivers in the region (Figure 10-G). Data for the whole river is useful in comparing to other rivers in the region and identifying clear deficiencies, such as wood debris abundance. However, data from analysis of specific segments will be used in the next section to identify areas of need and potential projects.

17 A) B) C) Figure 9. Pine River bedform delineation, bottom substrate, and in-stream fish cover.

18 Figure 10-A. Proportions of bedforms in the 11 trout streams (surveyed by MITU) in Northern Michigan, ordered by percent run bedform (black). Figure 10-B. Streambed substrate composition in the 11 trout streams (surveyed by MITU) in Northern Michigan, ordered by percent sand.

19 Figure 10-C. Hard and fine substrates composition in the 11 trout streams (surveyed by MITU) in Northern Michigan, ordered by percent fine substrate. Figure 10-D. Cumulative percent area of instream fish cover in the 11 trout streams (surveyed by MITU) in Northern Michigan, including deep water, wood debris and aquatic vegetation.

20 Figure 10-E. Percent area of deep water (>2.5 ft.) in the 11 trout streams (surveyed by MITU) in Northern Michigan. Figure 10-F. Percent area of wood debris in the 11 trout streams (surveyed by MITU) in Northern Michigan.

21 Figure 10-G. Percent area of aquatic vegetation in the 11 trout streams (surveyed by MITU) in Northern Michigan. Pine River Analysis: By Segment The Pine River was divided into 6 smaller segments for data analysis. Segment 1 consists of sites 1-4. These sites were grouped due to higher percentages of fine substrate and run habitat. Sites 5-8 were grouped into segment 2 due to an increase in hard substrate and riffle habitat relative to segment 1. Segment 4 consists of sites 9-12. They were separated from segment 2 because segment 3 has more riffles, less pools, and much less deep water than segment 2. Run habitat, fine substrate and deep water increases in sites 13-15 which are grouped into segment 4. Segment 5 is sites 16 and 17 where a decrease in run and increase in hard substrate relative to segment 5 is seen. Segment 6 is composed of site 18. Segment 6 is the lowermost reach of the river, and receives impoundment effects from Tippy Dam Reservoir, as well as receiving sand load from the entire watershed (Figures 5, 6 and 7). Bedform Structure Bedform diversity in the Pine River shows some clear differences between segments of the river (Figure 11). Segments 2 and 5 each have approximately 60% run habitat, with relatively larger proportions of riffles and pools, providing the best diversity of bedforms of all the segments. Segments 3 and 4 were slightly higher in run bedforms (70% and 75%) than 2, 3, and 5, but still provides significant riffle and pool habitats. Segment 1 had low bedform diversity with 89% run bedform present there. Segment 6, at the end of the river, had no bedform diversity, and was totally comprised of run bedform.

22 Figure11. Pine River bedform diversity. In-stream Habitat Availability The relative high abundance of deep water habitat in the Pine River extends to all segments except segment 6, the lowermost section (Figure 12). Segment 6 was low in deep water availability (9%), as well as wood (6%) and aquatic vegetation (5%). Elsewhere, deep water habitat was plentiful, averaging from 27 44% in segments 1 5. This is a very good fish habitat asset of the Pine River. Even in segments 1 and 4, which had higher proportions of run habitat, the percent deep water was 33% and 44% respectively. This indicates that while bedforms are dominated by runs, they are at least deeper habitat runs, as opposed to shallow and wide runs. Presence of deep water habitat is a function of the stream channel shape, and as such, where deep water habitat is lacking, it s often difficult to create, as it requires either narrowing the stream banks, or creating localized scouring of the streambed. The Pine River appears in good shape in regards to deep water habitat availability. The abundance of wood debris in the Pine River was generally low. Segment 1 had the highest average abundance of wood at 17%, which compared with other regional trout rivers surveyed, should be viewed as average or moderate. All other segments of the river contained 6 10% wood debris, which is quite low compared to other trout streams, resulting in the Pine having the lowest wood debris ranking of the rivers we ve surveyed to date (Figure 10-F). The slope and stream power of the Pine may be a factor that mobilizes wood debris here more than other rivers, leading to less residency time, and lower abundances. This will need to be evaluated further if wood additions are pursued. However, a rough comparison with other rivers of known high gradient, and high percentages of riffle/pool bedforms, like the Sturgeon and Pigeon Rivers, shows that the Pine River also has significantly lower wood debris abundance than them, indicating wood abundance in the Pine is likely deficient.

23 Figure12. In-stream habitat structure in the Pine River. Aquatic vegetation was highest in segment 1 (12%), and lowest in segment 5 (2%). For the rest of segments, it ranged between 5 7%, and was 6% for the entire river. When compared with other regional trout streams, all segments except segment 1 appear low or deficient in aquatic vegetation, a critical habitat element for juvenile trout and other fish species. Substrate Composition In general, the Pine River exhibits a good diversity of substrates within the streambed. Segments 2, 3, 4, and 5 exemplify this particularly well (Figure 13). Segment 1, did have considerably more sand present than segments 2-5, but still had significant proportions of gravel, cobble and boulders, and had the highest percentage of silt substrates of any segment. Silts are important substrates for many forms of burrowing mayflies, responsible for some of the best flyfishing hatches, (e.g., Ephemera, brown drakes, Hexagenia). In fact, segments 2-6 could be considered as having very little silt present, something that could possibly be linked to management of aquatic vegetation in the future, to improve conditions of both. Segment 6 was the one segment of the Pine River with a clear lack of substrate diversity (92% sand). This is the section of stream that receives the sand load from the rest of the watershed, but also is impacted in its transport capacity by the Tippy Dam backwaters. This section was also downstream of the Stronach Dam removal site, where sand from the former Stronach Dam impoundment was allowed to be transported naturally, and deposited in this river segment. The substrate composition of this segment is reflective of an over-abundance of sand sedimentation. From the data presented, sand over-abundance does not seem to be a primary limiting factor for the Pine River. There is ample area of gravel and larger substrates, and ample riffles as well. From what was

24 documented, these substrates and areas needed by lithophilic spawning fish species do not appear to be limiting in the Pine River. Figure 13. Pine River substrate composition by segment. Figure 14. Pine River fine (clay, silt, and sand) and hard (gravel, cobble, and boulder) substrate composition by segment. Recommendations and Management Actions When considered as a whole river, the Pine River appears generally to have good bedform diversity, very good substrate compositions of gravel, cobble and boulders, and ample deep water habitat available. However, it clearly is lacking wood debris compared with other regional trout streams. Additionally, the Pine appears to have low abundance of both silt substrates and aquatic vegetation (often related),

25 which are both related to shallower stream margin habitats, macroinvertebrate community diversity, and juvenile fish survival. We know that the Pine River has relatively high gradient or slope (total drop from headwaters to mouth is 417ft, average 10-15ft/mile) for the Lower Peninsula of Michigan, and has high contributions of groundwater to its flows. Water temperatures remain cold throughout its length, rarely exceeding 70 degrees F. Baseflows are relatively stable, and peak flows can be severe, (~10x the baseflow). With moderate flows and high gradient the river is expected to have high stream power and sediment transport capacity, in general. We also generally know from DNR and MSU fish surveys that the Pine produces lower densities of trout, but usually good to high survival rates of older age classes, compared to statewide averages. This general background understanding, taken with the results of this instream fish habitat assessment, may indicate that juvenile fish survival is limited due to lack of slow velocity areas with adequate cover (such as wood debris and aquatic vegetation beds). In general then, the clearest goals for improving fish habitat in the mainstem of the Pine may include additions of wood debris to improve fish cover, in both the deep and shallower water habitats. Additionally, it may well be worth pursuing the feasibility or viability of transplanting or augmenting aquatic vegetation beds. If appropriate microhabitats for their successful transplant could be identified, an increase in aquatic vegetation may help provide more juvenile fish cover, help collect and retain silts, create areas of slower water velocities, and possibly improve some nutrient retention. In addition, more vegetation may also create both food and substrates for enhanced macroinvertebrate communities. Wood Debris Enhancements Access The addition and management of wood debris are the clearest and best potential type of enhancement project for all sections of the Pine River. However, each section would need to be evaluated for the specific design and feasibility of pursuing wood debris additions, as each site will have unique access and design considerations and challenges. In considering access issues, the land ownership status will be important. According to the Pine River Natural River Plan (DNR Fisheries Division, 2003), the State of Michigan and the U.S. Forest Service have extensive land ownership, totaling approximately 35% of the Pine River corridor (Table 7). If work is pursued on state owned lands, early involvement and consent from DNR management staff is essential. Working on private lands will require the consent of willing landowners, which also necessitates early involvement and relationship building with the owners. Working on the abundant federal lands, will require that management staff from the US Forest Service agree with the need for the work, agree with the proposed designs for the work, and have appropriate lead time to complete the required permitting. Additionally, access will be challenging on certain segments of stream due to the physical or logistical limitations of access to the river with equipment appropriate for certain types of wood debris installation. For example, much of segment 5 is contained within steep river valley walls, with very limited access points.

26 Table 7. Landownership within the Pine River corridor in acres. Table taken from MDNR Fisheries Division, Pine River Natural River Plan (2003). Design Considerations In addition to access logistics, design of wood debris additions will need to consider both the physical carrying capacity of wood debris in each segment of the river, and also the social carrying capacity of wood debris in each segment of the river. By physical carrying capacity, we mean that given the general high slope and stream power of the Pine River, designs for the specific locations and installation techniques of the wood debris will be critical. In some sections of the Pine, it may be unrealistic to install large wood debris formations that will resist being mobilized by floods. Furthermore, where stability is sought, design specifications should utilize techniques that result in stabilized wood additions to prevent excessive movement or placed only partially in the water, trenched along the stream edge. Creating complex logjams using key pieces and a mixture of large diameter conifers and hard woods will maximize benefits to the fishery and ecosystem processes. Fine-tuned designs will be used to both identify areas where stable wood additions are appropriate and where intentionally mobile designs make sense. Social carrying capacity of wood debris will also need to be carefully discussed and addressed in design. The Pine River is a fast and challenging river for recreational floaters, therefore all wood debris formations will be constructed in a size and manner that will ensure safety and allow ample room for the passage of floaters and paddlers. Reasonably safe navigation on this river is necessary and may restrict wood debris additions to some extent. On the inverse side of the social carrying capacity consideration, is the clear evidence that the Pine ranks the lowest in wood debris of any of the rivers we ve surveyed to date in Northern Michigan (Figure 10-F). The only segment of the Pine which had average levels of wood, was segment 1, the furthest upstream segment and least utilized of the segments for recreational floating. All other segments had uniquely low amounts of wood debris. Both the Upper Manistee (a heavily used recreational floating river) and the Sturgeon River (comparable to the Pine in gradient and flow), both have approximately 20% wood on average, compared with the Pine River s average of 9%.

27 Designs for wood debris enhancements will need to honor the requirement for safe and reasonable passage for recreational floating, while balancing the ecological benefits to be derived from more wood debris. This balancing will only be accomplished by inclusive, respectful discussions among stakeholders and decision makers, and through creative wood debris enhancement designs. Aquatic Vegetation Enhancement Aquatic vegetation was low in all segments of the Pine except segment 1. We are not familiar, at this point in time, with pre-existing techniques or efforts to transplant or increase the establishment of aquatic vegetation beds in Michigan streams. However, if these techniques were developed, increasing the occurrence of aquatic vegetation in most of the Pine River could be an ideal priority project. These aquatic vegetation beds offer ideal juvenile trout and other fish habitat, as well as aiding retention of silts, forming slower water velocity microhabitats, and providing food and substrate for macroinvertebrates. Creating better juvenile trout habitat could be expected to boost overall trout survival and densities. Additionally, increasing aquatic vegetation would not pose any safety conflicts with recreational floaters. If there is interest in pursuing the feasibility of aquatic vegetation augmentation techniques, MITU will be glad to pursue a potential research study with partners. Segment 6. Segment 6, the lowermost segment of the river, stands in stark contrast to the other segments. This segment is 100% run bedform, dominated by sand substrate, with only 9% deep water, 6% wood debris, and 5% aquatic vegetation. This segment will continue to be challenged by it receiving the sediment load from entire watershed area upstream, and having diminished slope (and sediment transport capacity) because of the Tippy Dam impoundment effects that extend into this segment of river. For these reasons, this part of the river should not be expected to be restorable to conditions seen upstream of it. It will likely remain sediment impacted as long as current conditions persist (sediment load in the Pine stays the same, and Tippy Dam continues to exist). This section of river however, should be assumed important to fish migrations through it, from fish entering or leaving the Pine River to access either the habitat provided by Tippy Dam reservoir, and/or the segment of the Manistee River located upstream of Tippy Dam and downstream of Hodenpyle Dam. If particular portions of this segment 6 become homogenously wide and extremely shallow, it may deter certain fish species from migrating through it at certain times of year. Possible projects: 1.) Select placement of large wood debris formations to ensure localized scour pools or runs, to allow deep water habitats for fish migrating through this section. This would involve moderate to large wood debris pieces strategically placed in areas of big wide sand flats, to create small areas of deep water habitat throughout the segment 6. 2.) Relocating large wood debris back into the wetted stream channel. During the spring flood of 2014, following this in-stream fish habitat assessment, large pieces of wood debris from the river were mobilized. As high water receded, the mobilized large wood came to rest on the banks of the Pine River (particularly in segments 6 personal observation), at levels now above

28 the water line during normal flows. This loss of wood debris to fish habitat may be addressed through crews manually moving large wood debris pieces back into the stream, via power winches. The large sizes of this material would help re-create localized scouring if put back into the stream channel. Overall Prioritization Prioritizing protection and enhancement efforts is often a difficult process, which by necessity needs to explicitly consider: 1.) current status of the river and its fisheries, 2.) benefits to be derived by the activities, 3.) risk of creating unintended negative consequences, 4.) feasibility of the projects contemplated including coordination & management, funding, permitting and regulations, and access, 5.) the array of stakeholder values and motivations for undertaking such efforts. This habitat assessment report is intended to help contribute to elements 1, 2, and 3. Elements 4 and 5, along with the others, will be up to all those engaged in stewardship of the Pine River to consider. With that said, from the results of this in-stream fish habitat assessment, the following general priorities are offered as a starting place for further discussions that follow. Detailed maps of habitat conditions in each segment are included in Appendix 1 to aid in the refined selection of sites for future work. MITU staff will be available to produce specific data and graphics needed for projects that may not be included in this report, and also to participate in discussions, planning and implementation of work chosen to be pursued. - Develop a refined wood debris enhancement plan for the mainstem of the Pine River, and perhaps key tributaries. This would use detailed site specific information documented by this study, address and identify key priority areas, and key feasible areas. The report would address design alternatives that would increase the Pine River s wood debris abundance, while honoring feasibility issues, safety issues, logistic issues, and means to evaluate any efforts for effectiveness. Once target areas are identified, follow up field surveys may need to be done in recognition that the 2014 flood significantly redistributed wood debris in the river. The development of this report would be a vehicle for partner collaboration and discussions. - Investigate the feasibility of transplanting and/or promoting increased areas of aquatic vegetation. Aquatic vegetation serves as high quality juvenile fish cover and may be possible to promote in portions of wide/shallow stream channels otherwise lacking suitable fish habitat. While this may not increase suitability to larger trout, it could help ensure optimal juvenile rearing habitat within the river, which translates to better survival into older ages. - Ensure that sand from either upstream, severe bank erosion sites, roads, or other sources are prevented from delivering sand to this section of stream. Road crossing inventories for the watershed should be reviewed to identify remaining priorities. Bank erosion inventories should be reviewed for priorities. Tributaries contributing significant sediment into the mainstem should be evaluated for action.

29 - Consider evaluating significant tributaries of the Pine River. The Pine River is generally considered to have several tributaries that offer high quality coldwater fish habitat. Thought should be given to evaluating some of these. Literature Cited Our purpose was not to summarize all pertinent information and data for this river, so these references are limited and should not reflect all the applicable information available on this topic or for this river. Bryant, M.D. 1983. The Role of Management of Woody Debris in West Coast Salmonid Nursery Streams. North American Journal of Fisheries Management 3:322-330. Michigan Department of Natural Resources, Fisheries Division. 2003. Pine River Natural River Plan. Roni, P and T.P. Quinn. 2001. Density and size of juvenile salmonids in response to placement of large woody debris in western Oregon and Washington streams. Canadian Journal of Fisheries and Aquatic Science 58:282-292. Tonello, M. 2005. Little Manistee. Status of the Fishery Resource Report. MI DNR. 2005-08. Found at https://www.michigan.gov/documents/2005-8_little-manistee_river_144067_7.pdf. Zorn, T.G., P.W. Seelbach, and M.J. Wiley. 2009. Relationships between habitat and fish density in Michigan streams. Michigan Department of Natural Resources, Fisheries Report 2091, Ann Arbor. Zorn T.G. and M.J. Wiley. 2004. Untangling relationships between river habitat and fishes in Michigan s Lower Peninsula with covariance structure analysis. Michigan Department of Natural Resources, Fisheries Research Report 2073, Ann Arbor.

30 Appendix 1. Frequency distribution plots, for the number of bedform units in each segment of the Pine River, containing different percentages of area of wood debris, in 10% increments.

31 Segment 1.

32 Segment 2.

33 Segment 3.

34 Segment 4.

35 Segment 5.

36 Segment 6.

37 Other charts and maps are available upon request. For example, we have substrate compositions for each bedform unit in each section, and also made note of bank conditions (if significant erosion was noted, picture were also taken). GPS coordinates are also available for specific areas that ay be of interest in these charts, for planning purposes. Below are two examples, but they are omitted here for brevity. Please contact us at www.michigantu.org, if you desire specific report outputs.

38 Appendix 2. Road Stream Crossings Assessments If road crossings are undersized, they may not allow natural levels of sediment transport. This can lead to fine sediments accumulating immediately upstream of the crossing, while a scour pool can be created immediately below the crossing. In these cases, we d expect to observe: Upstream: - Higher abundance of fine substrates like sand and silt (relative to that seen further upstream) - A widening of the stream width relative to further upstream - Loss of slope upstream would result in run bedforms Downstream: - Coarser substrates, or higher abundance of hard substrates, as fine sediment is not transported through the crossing naturally, erosion results, leaving coarser substrates. - With scour pool creation, we d expect to see pool bedforms immeidately downstream of the corssing, followed by more run bedforms. - A decrease in stream width, as the stream scours deeper, width should decrease. In addition to undersized road crossings, improper design of road-stream crossings can result in fine sediments being delivered to the stream from the banks, or road approaches, or road surface itself. In these cases, we d expect to see higher abundances of fine substrates such as sand, downstream of the crossings, as compared with further upstream, or further downstream. Since these aspects of streams were measured in this assessment, this appendix provides charts of the conditions of bedforms, substrates, and stream widths around crossings that were encountered. 4 sections were analyzed for each: immeidately upstream of the crossing, immediately downstream of the crossing, and further upstream and downstream of each crossing (to represent zones further removed from the influence of the crossings).

39 17 Mile Rd. Crossing Some indication of slight under-sizing possible, as well as sedimentation.

40 Raymond Rd. Crossing

41 6 Mile Rd Crossing Width indicates some undersizing issues.

42 Skookum Rd Crossing Slight indications of undersizing potential in bedforms and substrates.

43 State Rd Crossing

44 10 Mile Rd Crossing

45 No. 50 Rd. Crossing

46 Peterson Bridge

47 Low Bridge this crossing was being replaced during the survey time period.