Res-Ashbridge1988 Survey of Potential and Available Salmonid

Volume 072 Article 01

FEDERAL AID IN FISH RESTORATION

SURVEY OF POTENTIAL AND AVAILABLE SALMONID HABITAT IN THE BOISE RIVER

Job Completion Report Project F-71-R-12, Subproject III, Job No. 3

Prepared for:

IDAHO DEPARTMENT OF FISH AND GAME

G. Asbridge and T.C. Bjornn

Idaho Cooperative Fish and Wildlife Research Unit University of Idaho Moscow, Idaho 83843

June 1988

TABLE OF CONTENTS

ABSTRACT ...... 1

OBJECTIVES ...... 2

RECOMMENDATIONS ...... 2

INTRODUCTION ...... 3

STUDY AREA ...... 5

TECHNIQUES ...... 11

Habitat classification survey ...... 11 Physical habitat measurements ...... 12 Water temperature ...... 17 Estimates of fish abundance ...... 17 Identification of limiting factors ...... 19 Identification of improvement measures ...... 19

FINDINGS ...... 20

Habitat classification survey ...... 20 Physical habitat measurements ...... 28 Width ...... 28 Depth ...... 30 Water velocity ...... 30 Substrate composition ...... 44 Cover ...... 52 Water temperature ...... 56 Fish abundance ...... 56 DISCUSSION ...... 64

LITERATURE CITED ...... 68

LIST OF TABLES

1. Visual substrate codes used on the Boise River and Loggers Creek during the summer of 1986 and 1987. The dominant substrate size class was recorded as X, and Y was the percent embeddedness of X ...... 12

2. Visual bank and instream cover codes used for seven sites on Loggers Creek during the summer of 1986. Cover objects were anything providing a significant velocity shelter or visual barrier for juvenile fish...... 14

3. Visual bank and instream cover codes used on the Boise River and three sites on Loggers Creek during the summers of 1986 and 1987. Variables were recorded as X/Y/Z where X was cover status, Y was the dominant cover type, and Z was the percent of Y in each cell. Cover objects were anything providing a significant velocity shelter or visual barrier for juvenile fish. Aquatic vegetation was counted only if it provided cover. Canopy had to be greater than 3 m above the water surface and breaking the planes of the cell ...... 14

4. Number of pool, run and riffle habitat units measured for detailed analysis and total number of transects established for those units in the five Boise River sections and Loggers Creek during summer, 1986 and 1987, and during October 1987 for Boise River sections 1 and 2 ...... 16

5. Number of classifications made during habitat classification surveys on the Boise River and Loggers Creek in 1986 and 1987 ...... 23

6. Estimated surface areas (m2) and associated standard deviations (in parentheses) of pool, run and riffle habitat in the Boise River and Loggers Creek during the summer flow period ...... 24

7. Mean habitat type surface areas (m2) and associated standard deviations (in parentheses) in the Boise River and Loggers Creek during the summer flow period ...... 25

8. Mean habitat unit widths (m), lengths (m), standard errors (in parentheses), the number of transects used for width calculations and the number of habitat units for length calculations for each Boise River study section and the study area during 1986 and 1987 summer flow periods. Boundary transects were included for width mean and range calculations ...... 26

9. Estimated numbers and associated standard deviations (in parentheses) of pool, run and riffle habitat units in the Boise River from Barber Dam to Star and Loggers Creek during summer, and for Boise River sections 1 and 2 during low flow periods. Only one pool was surveyed in section 1 during the low flow period, therefore a pool standard deviation was not calculated. No riffles were surveyed in section 2 during the low flow period so a number estimate was not possible ...... 27

10. Mean habitat unit widths (m), lengths (m), depths (m), velocities (m/s), ranges, and number of measurements for Loggers Creek. Width measurements equalled the number of transects per habitat type surveyed, length measurements equalled the number of habitat units surveyed (except pools where one length was not measured), depth and velocity measurements were taken at numerous points along each transect. Boundary transects were included for width calculations, but not for depth and velocity calculations. Habitat units were surveyed during the summer of 1986 ...... 28

11. Mean widths, depths and velocities for habitat units measured during summer and October, 1987, in the Boise River. Boundary transects were included to calculate means. For each habitat unit n = 3. Vertical lines to the right of two values indicate no significant difference between the values (alpha 0.05, paired t test) ...... 42

12. Mean habitat type depths (m), velocities (m/s), ranges (in parentheses), and number of measurements for Boise River sections and study area for 1986 and 1987 summer flow periods. Boundary transects were excluded when calculating means and ranges ...... 43

13. Percent relative abundance of three water velocity classes presented graphically in Figures 12, 14, 16, and 25 for two pools and two runs in the Boise River. Water velocity was measured every 15.2 cm depth interval of each vertical during the summer of 1987 ...... 52

14. Number of salmonids collected by electrofishing from six sites in the Boise River on 25, 26, and 27 October, 1986 while flows were low (169 cfs at Barber Park and 145 cfs at Glenwood Bridge) ...... 62

15. Number of salmonids counted by snorkeling in Boise River and Loggers Creek study sites during August 1986. Mountain whitefish size classes were 0 to 100 mm (age 0), 101 to 200 mm (age 1), and > 200 mm (age 2+). Rainbow and brown trout size classes were 0 to 85 mm (age 0), 86 to 200 mm (age 1), and > 200 mm (age 2+) ...... 63

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LIST OF FIGURES

1. Unregulated and regulated discharge of the Boise River at Lucky Peak Dam for water years 1986 and 1987. Unregulated discharge is calculated by the United States Army Corps of Engineers and simulates natural flow in the river without the three upstream dams ...... 4

2. Map of the Boise River from its origin at Lucky Peak Dam to Star, Idaho. The study area extended from Barber Dam to Star, a distance of 40.2 kilometers ...... 6

3. Boise River mean daily discharge from Lucky Peak Dam and at the At Boise gaging station during water years 1978 through 1982 ...... 7

4. Boise River mean daily discharge from Lucky Peak Dam and at the Glenwood Bridge gaging station for water years 1983 through 1987 ...... 8

5. Boise River mean daily discharge from Lucky Peak Dam and at the Glenwood Bridge gaging station for water years 1986 and 1987 ...... 9

6. Schematic diagram of a study site in the Boise River and Loggers Creek with three transects. Areas 1, 2 and 3 were the sums of cell areas associated with transects 1, 2 and 3, respectively ...... 13

7. Major irrigation diversions and electronic temperature recorder locations in the Boise River from Lucky Peak Dam to Star ...... 18

8. Relative abundance of pool, run and riffle habitat in the Boise River and Loggers Creek, including associated 95% confidence intervals. Summer habitat classification surveys were completed during June and July 1986; low flow surveys were completed in December 1986, April 1987 and October 1987 ...... 21

9. Relative abundance of pool, run and riffle habitat in Boise River sections during summer (top) and low flow (bottom) periods, including 95% confidence intervals. Summer habitat classification surveys were completed during June and July 1986, and low flow surveys were completed in December 1986, April 1987 and October 1987 ...... 22

10. Mean study section widths, depths, and habitat type velocities in each section in the Boise River from Barber Dam to Star. Measurements were taken during 1986 and 1987 summers. A horizontal line across two or more bars indicates no significant difference between those sections or habitat types ...... 29

11. Overhead map with depth isopleths of Pool 3, section 1 in the Boise River which was surveyed in August and October 1987...... 31

12. Transect cross sections from Pool 3, section 1 in the Boise River in summer and October 1987. For summer cross sections the clear areas had velocities < 0.20 m/s, cross hatched areas had velocities from 0.20 to 0.40 m/s and black areas had velocities > 0.40 m/s. In October, velocity was taken at 0.6 total depth so only wetted perimeter, depth and mean transect water velocity (calculated with 0.6 depth velocities) can be compared between summer and October. Sample sizes (n) were the number of measurements across each transect ...... 32

13. Overhead map with depth isopleths of Pool 2, section 2 in the Boise River which was surveyed in August and October 1987...... 33

14. Transect cross sections from Pool 2, section 2 in the Boise River in summer and October 1987. For summer cross sections the clear areas had velocities < 0.20 m/s, cross hatched areas had velocities from 0.20 to 0.40 m/s and black areas had velocities > 0.40 m/s. In October, velocity was taken at 0.6 total depth so only wetted perimeter, depth and mean transect water velocity (calculated with 0.6 depth velocities) can be compared between summer and October. Sample sizes (n) were the number of measurements across each transect ...... 34

15. Overhead map with depth isopleths of Run 2, section 1 in the Boise River which was surveyed in June and October 1987...... 35

16. Transect cross sections from Run 2, section 1 in the Boise River in summer and October 1987. For summer cross sections the clear areas had velocities < 0.20 m/s, cross hatched areas had velocities from 0.20 to 0.40 m/s and black areas had velocities > 0.40 m/s. In October, velocity was taken at 0.6 total depth so only wetted perimeter, depth and mean transect water velocity (calculated with 0.6 depth velocities) can be compared between summer and October. Sample sizes (n) were the number of measurements across each transect ...... 36

17. Overhead map with depth isopleths of Riffle 1, section 1 in the Boise River which was surveyed in June and October 1987 ...... 37

18. Transect cross sections in Riffle 1, section 1 in the Boise River in summer and October 1987. Water velocities were taken at 0.6 total depth only in summer and October. Sample sizes (n) were the number of measurements across each transect ...... 38

19. Mean habitat type depths (top) and velocities (bottom) in the Boise River. Measurements were taken during 1986 and 1987 summers. All habitat types were significantly different for depth (P<0.01) and velocity (P<0.05) ...... 39

20. Depth class frequency distributions for pool, run and riffle habitats in the Boise River. Measurements were taken during 1986 and 1987 summers and in October 1987 when flows were low in the river. Sample sizes (n) indicate the number of measurements; boundary transects were excluded ...... 40

21. Depth class frequency distributions for pool, run and riffle habitats in Loggers Creek. Measurements were taken in summer 1986. Sample sizes (n) indicate the number of measurements; boundary transects were excluded ...... 41

22. Velocity class frequency distributions for pool, run and riffle habitats in the Boise River. Measurements were taken during 1986 and 1987 summers and in October 1987 when flows were low in the river. Sample sizes (n) indicate the number of measurements; boundary transects were excluded ...... 45

23. Transect cross sections from Run 3, section 5 in the Boise River in summer 1987. Clear areas had velocities < 0.20 m/s, cross hatched areas had velocities from 0.20 to 0.40 m/s and black areas had velocities > 0.40 m/s. Mean transect velocities were calculated using 0.6 total depth velocities. Sample sizes (n) were the number of measurements across each transect ...... 46

24. Velocity class frequency distributions for pool, run and riffle habitats in Loggers Creek. Measurements were taken in summer 1986. Sample sizes (n) indicate the number of measurements; boundary transects were excluded ...... 47

25. Mean water column velocities, calculated from velocities measured every 15.2 cm, versus velocities taken at 0.6 total depth for one transect from three separate study sites ...... 48

26. Relative abundance of six substrate classes surveyed in the Boise River during 1986 and 1987 summers. Substrate class was estimated visually and only the dominant substrate class was recorded at each vertical. Sample sizes (n) indicate the number of measurements; boundary transects were included ...... 49

27. Relative abundance of six substrate classes by habitat type in the five Boise River sections and Loggers Creek. Substrate class was estimated visually during 1986 and 1987 summers, and only the dominant substrate class was recorded at each vertical. Sample sizes (n) indicate the number of measurements; boundary transects were included ...... 50

28. Relative abundance of six substrate classes by transect in the five Boise River habitat units previously described. Measurements were taken during summer 1987. Sample sizes (n) indicate the number of measurements; boundary transects were included ...... 51

29. Percent embedded by fines of the four larger substrate classes in the Boise River (top) and Loggers Creek (bottom) during 1986 and 1987 summers. Embeddedness was estimated visually and only applied to the dominant substrate class. Sample sizes (n) indicate the number of measurements; boundary transects were included ...... 53

30. Relative abundance of major cover types in the Boise River and Loggers Creek. A different cover classification system was used on seven Loggers Creek study sites, accounting for the difference in the number of major cover types in Loggers Creek and the Boise River. Both (Overhead) and Both (Instream) classifications in the Boise- River had a combination of instream and overhead cover in the cell but overhead or instream cover was dominant, respectively. In Loggers Creek Both refers to instream and overhead cover present in the cell, but the dominant type was not specified. Numerical values above bars indicate approximate surface areas (m2) with that cover type dominant in habitat units surveyed. The total surface area associated with some type of cover is given for habitat units surveyed in Loggers Creek ...... 54

31. Relative abundance of major cover types in Boise River study sections. Both (Overhead) and Both (Instream) classifications in the Boise River had a combination of instream and overhead cover in the cell but overhead or instream cover was dominant, respectively. Numerical values above bars indicate approximate surface areas (m2) with that cover type dominant in habitat units surveyed ...... 55

32. Relative abundance of major cover types in the five habitat units in the Boise River previously described for depth and velocity. Study sites were surveyed in summer 1987. Both (Overhead) and Both (Instream) classifications had a combination of instream and overhead cover in the cell but overhead or instream cover was dominant, respectively. Areas 1, 2 and 3 are sums of cell areas containing cover associated with transects 1, 2 and 3, respectively ...... 57

33. Mean daily water temperature at five locations in the Boise River from 2 July, 1986 to 27 October, 1987. The horizontal dashed line indicates the approximate upper preferred temperature for salmonids ...... 58

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34. Daily maximum and minimum water temperatures at Barber Park, near Glenwood Bridge, Eagle Road in the North Channel, Phylliss Canal diversion dam in the South Channel, and near Star in the Boise River from 2 July, 1986 to 27 October, 1987. The horizontal dashed line indicates the approximate upper preferred temperature for salmonids ...... 59

35. Cumulative temperature units (1 unit for each OC above 0 OC each day) for two sites in July and August 1986 and five sites in July and August 1987 ...... 60

36. Length frequency distributions of salmonids caught electrofishing at six sites in the Boise River on 25, 26 and 27 October, 1986 ...... 61

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ABSTRACT

A habitat classification survey, physical habitat measurements, and salmonid relative abundance estimates were completed in the summer and fall of 1986 and spring, summer, and fall of 1987. When discharge averaged 4430 cfs (124.0 m '/s) out of Lucky Peak Dam, runs were the most abundant habitat type in the study area except in the North Channel around Eagle Island and from the lower end of Eagle Island to Star where pools were the most abundant. When discharge averaged 180 cfs (4.7 m3/s) out of Lucky Peak Dam, pools were the most common habitat type in the study area. In many areas, during the summer months, water velocities were above the reported preferred range for rainbow and brown trout. Summer water temperatures increased downstream, were highest at Star, and were above optimum levels for trout growth downstream from Glenwood Bridge in an extended period during late summer and early fall. Cobbles (63.5 - 254.0 mm in diameter) were the dominant substrate, and the stream-bottom lacked roughness elements. In ten study sites surveyed in October, after flows were reduced, wetted width, mean depth, and water velocity decreased from summer values. Reliable counts of salmonid abundance were not possible with snorkel gear because visibility was limited by the slight turbidity of the water. In electrofishing samples collected from six sites in October, mountain whitefish were the most abundant salmonid followed by juvenile brown and adult rainbow trout.

OBJECTIVES

1. To conduct a habitat survey of the Boise River from Barber Dam to Star, Idaho, to estimate available salmonid habitat.

2. To assess relative abundance of salmonids in this section of the Boise River.

3. To identify limiting factors to production and rearing of wild rainbow and brown trout.

4. To identify measures needed to improve trout production.

RECOMMENDATIONS

Begin a habitat improvement program in the Boise River to increase the amount of.summer and winter rearing habitat.

Concentrate spawning habitat improvements in Loggers Creek and side channels of the Boise River.

Work to protect and enhance existing riparian vegetation and improve areas with little or no riparian vegetation.

Explore possibility of introducing a new hatchery strain of rainbow trout better adapted to temperature extremes.

Inform anglers of mountain whitefish abundance and habits to increase the yield of this species.

INTRODUCTION

The study reported herein was part of a larger study on the Boise River conducted by the Idaho Department of Fish and Game. This study was undertaken to assess and quantify available salmonid habitat in the river from Barber Dam to Star, Idaho. Results of this study along with data from a creel census and salmonid population estimates will be used to formulate a comprehensive management plan for the Boise River.

Residents of the Boise Valley enjoy and benefit from the Boise River as a source of recreational and agricultural water. The river is unique because it has been, and continues to be, a haven for wildlife of all kinds. The demand for irrigation water began in the mid 1800's, and the Boise River reservoir system has since grown to meet increased irrigation and flood control needs (U.S. Army Corps of Engineers 1985). Early projects were built solely to supply irrigation water to the Boise Valley and included Diversion Dam, New York Canal, and Lake Lowell - finished in 1908, and Arrowrock Dam - completed in 1915. Later, Anderson Ranch Dam was built as a multipurpose project providing irrigation water, electrical power, and recreation. Lucky Peak Dam, finished in 1954, was built primarily for flood control, but a power generating facility was completed in 1987.

The system of reservoirs and diversion dams has altered the Boise River's natural flow regime, and, most likely, its temperature regime. Flows in the river today follow the same general pattern as the river before the dams but with important differences. Summer flows are kept at higher levels now because of irrigation needs, and, generally, winter flows are kept at a minimum while the upstream reservoirs are filled (Figure 1). Spring runoff is now controlled to prevent flooding in the Boise Valley except during low water years (Figure 1, water year 1987) when the need for flood control is not critical. Summer water temperatures are likely cooler now than during the period before Lucky Peak Dam because water is released from the cooler water at the bottom of the reservoir. Summer temperatures in the River Tees below Cow Green Reservoir were reduced after impoundment (Crisp 1977), as were summer temperatures in the Rogue River below Lost Creek Dam (Smith and McPherson 1981).

Although the Boise River flows through the most populated valley in Idaho and is popular with anglers, salmonid habitat research has been limited. Resource Systems Incorporated (1983), at the request of the City of Boise and Ada County, surveyed the river from Diversion Dam downstream through Eagle Island State Park and classified it into major wetland and deepwater zones using the United States Fish and Wildlife Service classification system outlined in "Classification of Wetlands and Deepwater Habitats of the United States" (Cowardin et al. 1979). This survey was general in nature, and there was no attempt to quantify salmonid (or other wildlife) habitat. Gibson (1975) assessed fish relative abundance and water quality in the river from Barber Dam downstream to the mouth, but he did not survey any habitat.

STUDY AREA

The Boise River flows westward out of Lucky Peak Dam for 102.6 km (63.8 mi) until it empties into the Snake River near Parma, Idaho. The study area extended from Barber Dam downstream to Star (river km 94.8 to 54.5), a distance of 40.3 km (25 mi) (Figure 2).

Flows in the river are regulated by releases from three dams: Anderson Ranch, Arrowrock, and Lucky Peak. Most of the natural runoff results from snow with high flows occurring each spring when temperatures increase and the snow melts. Typically, the annual high water period begins with a discharge increase in March or April, with the peak discharge between April 15 and July 15, followed by a gradual decrease to base flows during July and August (U.S. Army Corps of Engineers 1985) (Figures 3, 4, and 5). Low flows occur from September through February in most years. The above pattern is variable and depends largely on the amount of water accumulated in snow in the upper watershed and carryover water storage in the reservoirs.

Flows peak around 8,000 to 10,000 cfs at the Lucky Peak Dam outlet (Near Boise gaging station, river km 102.6) during spring runoff in an average water year, falling to 3,000 to 4,000 cfs during summer and 100 to 300 cfs in winter (Figure 3, water year 1981). In water years with a lower than average snow pack the peak spring runoff flows are reduced by 3,000 to 4,000 cfs, but flows during late summer and winter are similar to those in average water years (Figure 3, water year 1979). During above average water years flows may approach 14,000 cfs in the spring (Figure 4, water year 1983) but fall to approximately average levels in summer. For water years 1978 to 1987, flows during summer after the peak runoff have been similar.

During the irrigation season (April 15-October 15) irrigation diversions are significant, accounting for the average 2,600 .cfs difference between the Near Boise and Glenwood Bridge gaging stations (river km 102.6 and 76.4, respectively), and result in low flows near Star (river km 54.5). During winter, flows at both gaging stations are roughly equal regardless of runoff characteristics, but winter flows can vary from year to year (Figure 4) because of fluctuations in snow pack. The Idaho Department of Fish and Game has contracted for 50,000 acre-feet yearly for streamflow maintenance (U.S. Army Corps of Engineers 1985), most of which is used in winter during low flow periods.

The three reservoirs are operated as one system primarily to provide flood control and irrigation water to the Boise Valley. To provide for irrigation and recreation needs, water is stored in reservoirs from the end of each irrigation season (mid-October) until spring runoff is over. Boise River channel capacity varies between approximately 3,500 cfs and 10,000 cfs (U.S. Army Corps of Engineers 1985). Flows from 3,500 cfs to 6,500 cfs at Glenwood Bridge result in some minor flooding, although significant channel and bank erosion occurs at flows greater than 5,000 cfs. Flooding and damages increase with increased flows and show a marked rise when flows exceed 10,000

cfs. Gravel bar, tree, and brush accumulation within the channel are significant flood control constraints as is Eagle Island.

Water quality in the Boise River is generally high. As water leaves Lucky Peak Reservoir it has a high oxygen content, low BOD, low TDS, low bacteria levels, and nutrient levels below that needed to produce nuisance algal growth (U.S. Army Corps of Engineers 1985). Water quality decreases as it flows through the Boise Valley, partially because the river receives point and nonpoint pollution from two city wastewater treatment plants, storm drain discharges, sewage lagoon discharges, feedlot runoff, and irrigation returns (U.S. Army Corps of Engineers 1985). Low flow periods are most susceptible to decreases in water quality because of a lessened assimilative capacity. Ground water flows into the river have a DO deficit and adversely influence river DO (U.S. Army Corps of Engineers 1985). Irrigation returns are not a major water quality problem in the study area since most returns are downriver from Star.

The Boise River flows through the most populated valley in Idaho; Boise alone has a population of approximately 106,000 people. In addition to its importance for agriculture, the river provides Boise Valley citizens with an accessible recreational resource. Fishing, tubing, waterfowl hunting, and swimming are popular, and the river is used extensively in the spring, summer, and fall. The river is also open to fishing during winter.

Climate in the Boise Valley is characterized by hot, dry summers and cold winters. Broadleaf trees and assorted shrubs dominate the streamside vegetation, but as one moves away from the river, grasses and sagebrush dominate until the higher elevations where evergreens are most abundant.

Fish found in the study area include: rainbow trout Salmo gairdneri, brown trout Salmo trutta, mountain whitefish Prosopium williamsoni, bluegill Lepomis macrochirus, black crappie Pomoxis nigromaculatus, largemouth bass Micropterus salmoides, redside shiner Richardsonius balteatus, sucker Catastomus sp., carp Cyprinus carpio, chiselmouth Acrocheilus alutaceus, northern squawfish Ptychocheilus oregonensis, and sculpin Cottus sp. (Gibson 1975).

TECHNIQUES USED

The Boise River study area was divided into five sections: Barber Dam to Boise State University (river km 94.8 to 85.3, section 1), Boise State University to the upper end of Eagle Island (river km 85.3 to 74.0, section 2), the South Channel around Eagle Island (river km 74.0 to 61.1, section 3), the North Channel around Eagle Island (river km 74.0 to 61.1, section 4), and the lower end of Eagle Island to Star (river km 61.1 to 54.5, section 5). The entire length of Loggers Creek, a 4.2 km long side channel of the Boise River, was considered a separate study section.

Habitat classification survey

A habitat classification survey was used to estimate abundance of different habitat types at two flows in the river. The entire study area, including Loggers Creek, was surveyed-during late June and early July, 1986, when discharge from Lucky Peak Dam averaged 4430 cfs (124.0 m3/sec) (Figure 5). Barber Dam to the Settlers Canal diversion dam (river km 94.8 to 83.7) was urveyed December 30, 1986, when the discharge was 146 cfs (4.1 m3/s) out of Lucky Peak Dam. Settlers Canal diversion dam to Star (river km 83.7 to 54.5), excluding a 6.0 km section of the north channel around Eagle Island, was surveyed April 5 and 6, 1987, when the discharge was 204 cfs (5.7 m3/s) out of Lucky Peak Dam. The 6.0 km section in the north channel around Eagle Island was surveyed October 28, 1987, when the discharge from Lucky Peak Dam was 150 cfs (4.2 m3/s).

Pool, run, riffle, and pocketwater were the four types of habitat identified in this survey. Pools were sections with slow water velocity and were usually deeper than a riffle or a run; runs did not form distinguishable pools, riffles, or pocketwaters and had a rapid nonturbulent flow; riffles were sections where water velocity was fast, stream depths were relatively shallow and the water surface gradient was relatively steep; pocketwaters were riffle areas interspersed with small pools (Platts et al. 1983). Riffles were easily distinguished from other habitat units, but some pool and run sections could have been classified either way. In these situations surface velocity was the deciding factor; units with a predominant downstream current for the length of the unit were recorded as runs.

Surveyors walked along the river bank and classified the river into one of the four habitat types at every tenth step, except for the summer 1986 surveys of the Barber Park to the upstream end of the Greenbelt (river km 93.6 to 89.3) and Glenwood Bridge to Star (river km 76.4 to 54.5) sections that were surveyed using a raft or canoe because of the difficulty of hiking along the river. To improve the accuracy of surveying by raft, we surveyed selected river sections both on foot and by raft until we were able to get similar results. All low flow surveys were completed on foot.

After the survey was completed the percentage of the stream made up by..each habitat type (HT) was estimated as (Shepard 1983):

PHI = nHT / nTOT * 100 [Equation 1]

P Where: HT = percentage of habitat type "HT". n HT = number of habitat type "HT" enumerated. nTOT = total number of all habitat types enumerated.

Physical habitat measurements

To measure physical habitat variables we used a line transect method modified from Platts et al. (1983) and Bovee (1982). Each study site (a habitat unit) selected for transect measurement had a transect at the upstream and downstream hydrologic controls plus at least one other transect between the outer two. The number of transects depended on the length and complexity of the study site. Width, depth, velocity (measured at 0.6 water depth), substrate (Table 1), embeddedness, and cover (Tables 2 and 3) were measured across each transect at points where a noticeable change in one of the variables occurred. The point on the transect where the above variables were measured was called the vertical (Bovee 1983). The vertical marked the edge of a cell whose length was one half the distance to the adjacent upstream and downstream transects and whose width extended to the adjacent vertical on the left (looking upstream) (Figure 6). The sum of the cell areas associated with a single transect was termed Area 1-5, depending upon the transect (Figure 6). At nine representative study sites we measured velocity every 0.5 ft (15.2 cm) in the water column, in addition to the 0.6 depth measurement, to determine depth versus velocity profiles and 0.6 depth versus mean vertical velocity relationships.

Table 1. Visual substrate codes used on the Boise River and Loggers Creek during the summer of 1986 and 1987. The dominant substrate size class was recorded as X, and Y was the percent embeddedness of X.

X: 1. Silt or detritus - particulate organic matter. 2. Sand - less than 1.5 mm. 3. Pea gravel - 1.5 to 6.4 mm. 4. Pebble - 6.4 to 63.5 mm. 5. Cobble - 63.5 to 254.0 mm. 6. Boulder, bedrock - greater than 254.0 mm.

Y: 1. 0 - 24%: Rock bed, very few fines. 2. 25 - 49%: Can see most rocks and tell size. 3. 50 - 74%: Can see rocks but cannot tell size. 4. 75 - 100%: Can see only tops of rocks.

Table 2. Visual bank and instream cover codes used for seven sites on Loggers Creek during the summer of 1986. Cover objects were anything providing a significant velocity shelter or visual barrier for juvenile fish.

Instream cover: 1. Aquatic vegetation. 2L. Logs or debris (above water surface). 2B. Boulders or debris (above water surface). 3L. Logs or debris (below water surface). 3B. Boulders or debris (below water surface). 4. Man-made structures (bridge abutments, etc.). Bank cover: 1. Undercut bank, log or root mass. 2. Brush overhang 2 meters above water surface. 3. Brush overhang between 2 meters and canopy overstory. 4. Overstory canopy. 5. No cover.

Table 3. Visual bank and instream cover codes used on the Boise River and three sites on Loggers Creek during the summers of 1986 and 1987. Variables were recorded as X/Y/Z where X was cover status, Y was the dominant cover type, and Z was the percent of Y in each cell. Cover objects were anything providing a significant velocity shelter or visual barrier for juvenile fish. Aquatic vegetation was counted only if it provided cover. Canopy had to be greater than 3 m above the water surface and breaking the planes of the cell.

X: 1. No cover. 2. Instream (totally submerged). 3. Overhead (out of stream). 4. Both (cover in and out of stream).

Y: 1. No cover. 2. Small object (organic): 10-29 cm. 3. Large object (organic): >30 cm. 4. Small object (inorganic): 10-29 cm. 5. Large object (inorganic): >30 cm. 6. Aquatic vegetation. 7. Overhead cover <1 m above water surface (no canopy). 8. Overhead cover <1 m above water surface (with canopy). 9. Overhead cover 1-3 m above water surface (no canopy). 10. Overhead cover 1-3 m above water surface (with canopy). 11. Canopy cover >3 m above water surface. 12. Undercut bank.

Z: 1. 0 - 24% coverage in cell. 2. 25 - 49% coverage in cell. 3. 50 - 74% coverage in cell. 4. 75 - 100% coverage in cell.

Total wetted surface area of each of the five river sections was calculated as (Shepard 1983):

ATOT = (SL)(WTOT) [Equation 2] where: ATOT = total wetted surface area of the section. SL = total length of the section. WTOT = mean wetted width of the section.

The total wetted surface area of each habitat type in each section was calculated as: AHT = (PHT)(ATOT) [Equation 3]

A where: HT = total wetted surface area of habitat type "HT". P HT = percentage of habitat type "HT". ATOT total wetted surface area of the section.

Estimated total surface areas for each section were summed to estimate surface area of the entire study area. Habitat unit numbers within a section were then estimated as: NHT = AHT / aHT [Equation 4]

N where: HT = Number of habitat type "HT" within a section.

A HT = total wetted surface area of habitat type "HT". aHT = mean area of habitat type "HT" within a section.

Estimated habitat unit numbers were summed to obtain the estimated total number of habitat units in the study area.

The number of pool, run and riffle habitat units selected for detailed analysis within a study section was proportional to their relative abundance within that section as determined by the habitat classification survey (Table 4). Study sites on the Boise River and Loggers Creek were selected systematically (Scheaffer et al. 1986).

We were able to wade all study sites in Loggers Creek, but in the Boise River a raft or drift boat was used for many transects because the river was too deep or swift to wade. We devised a rope and pulley system similar to that described by Knudsen et al. (1984) to ferry the raft along each transect.

In October 1987, while discharge averaged 150 cfs (4.2 m3/s) out of Lucky Peak Dam, six sites in section 1 and four sites in section 2 (Table 4) that had been surveyed in summer were measured again to determine differences in physical habitat between high and low flow periods. Transects were placed in exactly the same positions in October as they were in the summer of 1987.

Table 4. Number of pool, run and riffle habitat units measured for detailed analysis and total number of transects established for those units in the five Boise River sections and Loggers Creek during summer, 1986 and 1987, and during October 1987 for Boise River sections 1 and 2.

Habitat unit

Pool Run Riffle Total

Section 1 Summer Number of units 4 6 3 13 Number of transects 12 21 11 44

October Number of units 22 2 6 Number of transects 6 6 6 18

Section 2 Summer Number of units 4 6 4 14 Number of transects 12 22 15 49

October Number of units 22 4 Number of transects 6 6 12

Section 3 Number of units 25 2 9 Number of transects 6 19 6 27

Section 4 Number of units 43 2 9 Number of transects 12 10 6 28

Section 5 Number of units 43 2 9 Number of transects 14 10 6 30

Loggers Creek Number of units 4 2 4 10 Number of transects 20 10 20 50

Four habitat units were measured in the Boise River in 1986, one run and riffle each in sections 1 and 2. The remaining habitat units were measured in 1987 (one run in section 2 was measured both years). Ten units were measured in Loggers Creek in 1986, but none were measured in 1987.

Analysis of variance (ANOVA) was run on all width, depth and velocity data to test the null hypothesis that there was no difference between means by section, habitat type and habitat type within a section. Boundary transect data was not used in depth and velocity analysis because these transects were not always indicative of the study site. The following model was used to test the above hypothesis:

Y = u + sec + hab + sec*hab + sec*hab*rep + sec*hab*rep*tran + error [Equation 5] where:

Y = dependent variable (width, depth or velocity). u = overall population mean. sec = study section effect. hab = habitat type effect. rep = habitat type effect within a section. tran = transect effect within a habitat unit. error = random error term.

For Loggers Creek data the sec term was not used. A paired t test was used (alpha = 0.05) to test for width, depth and velocity differences between high and low flows in the ten units surveyed in summer and October 1987.

Water temperature

Five electronic temperature recorders were placed in the Boise River to monitor daily and seasonal temperature fluctuations. Recorders were placed at Barber Park (river km 93.5) on 3 July, 1986; 1000 m upstream from Glenwood Bridge (river km 77.2) on 2 July, 1986; Phylliss Canal diversion dam in the South Channel around Eagle Island (river km 63.1) on 23 August, 1986; Eagle Road in the North Channel around Eagle Island (river km 69.2) on 30 December, 1986; and Star (river km 54.5) on 27 May, 1987 (Figure 7).

Estimates of fish abundance

Two of us snorkeled all habitat units that were measured for physical habitat variables in 1986. Whenever possible we snorkeled upstream, but if the current was too strong, or the depth over one meter, we snorkeled with the current. Three to four longitudinal transects per habitat unit were adequate in Loggers Creek; however, up to nine transects were required in Boise River habitat units due to river width and visibility. None of the habitat units measured in 1987 were snorkeled because the visibility was not good enough.

On 25, 26, and 27 October, 1986, sites at Barber Park, Municipal Park, Ann Morrison Park, Glenwood Road, Eagle Road (North Channel), and Linder Road (South Channel) were electrofished to determine relative abundance of salmonids and to obtain salmonid size class information. Each site, except Linder Road, was sampled using a five man crew that towed a small boat containing a 3500 watt generator, variable voltage pulsator, and plastic containers of water for the fish. Two people had

positive electrodes and two netted fish. The electrofishing unit was towed upstream in the middle of the channel. The two persons with electrodes moved back and forth across the stream ahead of the boat to fish the entire site. We picked sites with a riffle at the upstream end which acted as a natural barrier to fish movement. At Linder Road the water was too deep and swift to wade so two of us electrofished a 200 m section in a drift boat. We fished from one bank to the other in a zig-zag pattern so as to hit as much of the habitat as possible, but we were hampered with generator failures which shortened our sampling time. One pass was made at each of the six sites, but we did not keep time at any of the sites nor did we measure the length of each site (although we have approximate estimates). All salmonids were enumerated and measured to the nearest centimeter (total length), and an effort was made to distinguish between hatchery and wild rainbow trout.

To get an idea of hatchery rainbow trout movement and survival, 987 catchable sized rainbow trout were tagged with metal jaw tags and released into the Boise River at three sites. On 15 and 16 July, 1986, 331 fish were released at Barber Park (river km 93.6), 313 fish at Glenwood Bridge (river km 76.4), and 343 fish at the Star Bridge (river km 54.5). Signs were posted along the study area instructing anglers as to the purpose of the tagged fish and to return the tags to the Idaho Department of Fish and Game along with a description of where the fish was caught.

Identification of limiting factors

Trout production in the Boise River downstream from Barber Dam may be limited by temperature, quantity and quality of habitat, food abundance, and harvest rate. A literature search to ascertain those factors which limit trout production in rivers was conducted and the findings were compared with conditions found in the Boise River. Data from the habitat surveys can be used to determine conditions in the Boise River and lead to the identification of factors that may be limiting trout production.

Identification of improvement measures

Potential improvements in fish habitat are reviewed in the discussion section of this report.

FINDINGS

Habitat classification survey

Runs were the most abundant type of fish habitat in the Boise River study area and in Loggers Creek when discharges from Lucky Peak Dam averaged 4430 cfs (124.0 m3/s) (Table 5 and Figure 8). Sections 4 (North Channel) and 5 (lower end of Eagle Island to Star) were the only sections where pools were more abundant than runs (Figure 9). Most of the water flowing around Eagle Island was in the South Channel and much was diverted for irrigation before the lower end of Eagle Island. Flows of about 150 cfs in the North Channel and in the river near Star resulted in an increased likelihood of pool type habitat. A majority of the habitat in the upper two sections (Barber Dam to the upper end of Eagle Island) and the South Channel was classified as runs during the summer. Boise River flows downstream from Lucky Peak Dam during the summer survey averaged 1300 cfs (36.4 m /s)3at Barber Park, 840 cfs (23.5 m3/s) at Glenwood Bridge, 650 cfs (18.2 m3/s) at the Phylliss Canal Diversion Dam in the South Channel, and 150 cfs (4.2 m3/s) in the North Chanel and at Star. Flow in Loggers Creek was approximately 18 cfs (0.5 m3/s) during the survey.

New York and Ridenbaugh canals (Figure 7) divert approximately 3,150 cfs (88.2 m3/s) from the river upstream from Barber Park during the peak irrigation season. Bubb, Boise City, Settlers, Thurman Mill, and Farmers Union canals divert approximately 500 cfs (14.0 m3/s) between Barber Park and Glenwood Bridge. Between Glenwood Bridge and Star, approximately 775 cfs (21.7 m3/s) is diverted in the Ballentyne, Phylliss, Middleton and Hart-Davis canals. In addition to the above canals, there are numerous smaller canals throughout the study area. Water is added to the river from irrigation returns, groundwater and intermittent streams, although additions from irrigation within the study area are negligible as most of the irrigation returns occur below Star. When discharges from Lucky Peak Dam and flows at Glenwood Bridge averaged 180 cfs (5.0 m3/s) and 242 cfs (6.8 m3/s), respectively, in fall, winter, and early spring, pools were the most abundant type of habitat for fish in all five sections of the study area (Figures 8 and 9 and Table 5). The amount of habitat classified as riffle was similar in summer and winter. Much of the river classified as runs in summer was classified as pools in late fall, winter, and early spring. The upper sections of river were most affected by changes in habitat classification between summer and fall-winter periods because that is where flow differences were largest. Loggers Creek was not surveyed during winter when flows were low in the Boise River.

Table 5. Number of classifications made during habitat classification surveys on the Boise River and Loggers Creek in 1986 and 1987.

Number of classifications

Pool Run Riffle Total

Section 1 Summer 121 578 231 930 Low flow 780 211 252 1243

Section 2 Summer 286 640 353 1279 Low flow 704 195 280 1179

Section 3 Summer 237 757 221 1215 Low flow 527 479 239 1245

Section 4 Summer 707 414 342 1463 Low flow 1026 141 243 1410

Section 5 Summer 370 222 222 814 Low flow 503 100 131 734

Study area Summer 1721 2611 1369 5701 Low flow 3540 1126 1145 5811

Loggers Creek Summer 140 253 104 497

Runs made up a larger portion of the total surface area in sections 1, 2, and 3 of the Boise River and Loggers Creek than pools and riffles (Table 6). In Boise River sections 4 and 5 pools made up the largest part of the surface area. Pools and riffles were generally shorter and less numerous than runs, thus they had less surface area. Mean run surface area was larger than mean pool and riffle surface area in sections 1, 3, and 5 of the Boise River and in Loggers Creek, and mean pool surface area was largest in sections 2 and 4 (Table 7). Mean riffle surface area was smallest in the Boise River, except in section 2, and in Loggers Creek.

Table 6. Estimated surface areas (m2) and associated standard deviations (in parentheses) of pool, run and riffle habitat in the Boise River and Loggers Creek during the summer flow period.

Surface area

Pool Run Riffle Total

Section 1 50774 242542 96933 390249 (42) (23) (28)

Section 2 101771 227739 125612 455122 (16) (18) (41)

Section 3 48475 154835 45203 248513 (2) (2) (5) Section 4 145464 85180 -70366 301010

(7) (9) (8) Section 5 86138 51683 51683 181726 (14) (20) (26)

Study area 478294 725640 380468 1584402

(9) (9) (15) Loggers Creek 4477 8090 3326 15893 (0.6) (0.3) (0.4)

Table 7. Mean habitat type surface areas (m2) and associated standard deviations (in parentheses) in the Boise River and Loggers Creek during the summer flow period.

Surface area

Pool Run Riffle

Section 1 4876 8850 2377 (3067) (4827) (1132)

Section 2 6151 4388 4727 (3251) (1607) (889)

Section 3 1049 4722 660 (43) (2375) (284)

Section 4 3994 2882 756 (1246) (1903) (26)

Section 5 2123 4043 611 (560) (2664) (116)

Study area 3927 5342 2314 (2640) (3501) (1929)

Loggers Creek 118 188 44 (80) (67) (15)

Based on mean length of each type of habitat (Table 8) and their proportion in the river (Table 5), I estimated riffles were more numerous than pools or runs in the study area, except in section 1 during the low flow period and section 2 during the summer (Table 9). No riffles were measured in section 2 in October 1987, so their number could not be estimated for the low flow period. Riffles were the most numerous type habitat, despite making up a low percentage of the river length, because of their short length. Estimated numbers of pool and run habitat units followed similar trends as their respective percentages in the river (Figure 9) during summer and low flow periods.

Table 8. Mean habitat unit widths (m), lengths (m), standard errors (in parentheses), the number of transects used for width calculations and the number of habitat units for length calculations for each

26 Boise River study section and the study area during 1986 and 1987 summer flow periods. Boundary transects were included for width mean and range calculations.

Pool Run Riffle

N Width Length N Width Length N Width Length

Section 1 Transects 12 40.7 111.3 21 42.8 198.7 11 40.3 57.4 Habitat units 4 (11.3) (40.5) 6 (13.4) (118.7) 3 (10.8) (23.0)

Section 2 Transects 12 41.1 147.4 22 32.9 137.0 15 44.6 108.7 Habitat units 4 (6.9) (75.3) 7 (14.5) (51.9) 4 (17.7) (44.4)

Section 3 Transects 6 23.9 43.9 19 21.2 221.8 6 23.0 28.2 Habitat units 2 (1.4) (1.7) 5 (3.4) (106.9) 2 (3.0) (8.8)

Section 4 Transects 12 25.5 154.8 10 21.7 124.8 6 21.9 34.9 Habitat units 4 (7.0) (32.4) 3 (8.8) (56.6) 2 (6.7) (4.5)

Section 5 Transects 14 25.2 86.3 10 34.6 128.4 6 27.1 21.8 Habitat units 4 (10.4) (31.0) 3 (8.5) (105.9) 2 (14.1) (2.4)

Study area Transects 56 31.8 115.9 82 31.6 167.5 4 35.1 60.6 Habitat units 18 (11.6) (55.3) 24 (13.8) (92.9) 13 (15.8) (43.6)

Table 9. Estimated numbers and associated standard deviations (in parentheses) of pool, run and riffle habitat units in the Boise River from Barber Dam to Star and Loggers Creek during summer, and for Boise River sections 1 and 2 during low flow periods. Only one pool was surveyed in section 1 during the low flow period, therefore a pool standard deviation was not calculated. No riffles were surveyed in section 2 during the low flow period so a number estimate was not possible.

Estimated number

Pool Run Riffle

Section 1 Summer 10 (6) 27 (15) 41 (19) Low flow 47 8 (1) 51 (20)

Section 2 Summer 16 (9) 52 (19) 27 (27) Low flow 55 (48) 12 (2)

Section 3 Summer 46 (2) 33 (16) 68 (29)

Section 4 Summer 36 (11) 29 (20) 93 (3)

Section 5 Summer 41 (11) 13 (8) 85 (16)

Study area Summer 149 (82) 154 (89) 314 (137)

Loggers Creek Summer 38 (26) 43 (15) 76 (26)

Runs were longer than pools and riffles in sections 1, 3, and 5 while pools were the longest habitat type in sections 2 and 4 (Table 8). Riffles were the shortest habitat type in all five sections. In Loggers Creek runs were the longest habitat type followed by pools and riffles (Table 10).

Table 10. Mean habitat unit widths (m), lengths (m), depths (m), velocities (m/s), ranges, and number of measurements for Loggers Creek. Width measurements equalled the number of transects per habitat type surveyed, length measurements equalled the number of habitat units surveyed (except pools where one length was not measured), depth and velocity measurements were taken at numerous points along each transect. Boundary transects were included for width calculations, but not for depth and velocity calculations. Habitat units were surveyed during the summer of 1986.

Parameter Pool Run Riffle

Length Mean 28.4 51.7 13.8 Range 9.1-45.5 30.5-73.0 11.0-18.6 N 2 3 4

Width Mean 4.6 3.9 3.2 Range 2.6-7.5 2.7-5.1 2.0-5.9 N 20 10 20

Depth Mean 0.58 0.45 0.33 Range 0.0-1.6 0.0-0.9 0.01-0.7 N 191 97 175

Velocity Mean 0.14 0.18 0.29 Range 0.0-0.8 0.0-0.8 0.0-1.3 N 191 97 175

Physical habitat measurements

Width. - The Boise River was widest in study sections 1 and 2 and narrowest in sections 3 and 4 for all three types of habitat (Table 8). In section 5 the river widened, but, except for runs, was not as wide as in sections 1 and 2. Section 1 was significantly different than sections 3, 4, and 5 and section 2 was significantly different than sections 3 and 4 (P<0.01, Figure 10). Within sections, widths of each type of habitat were similar, except in sections 2 and 5 where runs were narrower and wider than pools and riffles, respectively, but they were not significantly different from either. For the entire study area mean pool, run and riffle widths were not significantly different. Mean widths of pools were wider than runs or riffles in Loggers Creek, but the differences were not significant (Table 10).

During October 1987, when flows were low, the ten habitat units surveyed had narrower mean widths than the same units in summer 1987 (Table 11). For runs 1, 2, and 3 in section 1 the differences were significant (alpha = .05). In four habitat units presented graphically which were surveyed in summer and October (Figures 11-18), width reductions varied between habitat units and transects within habitat units and depended on channel morphology at the transect. In areas near the banks where depths were shallow the reductions in width from summer to October were greater.

Depth. - Section 1 was significantly deeper than sections 2, 4, and 5 in the Boise River (P<0.01, Figure 10). Section 3 was significantly deeper than sections 4 and 5. When summed over the entire study area, pools, runs and riffles were all significantly different from each other in terms of depth (P<0.01, Figure 19). Pools were the deepest habitat type in all sections followed by runs and then riffles, except in section 2 where riffles were deeper than runs, but the differences were not significant (Table 12). Pool depths in summer reached 3.0 m, but the deepest vertical in October was 2.0 m (Figure 20). Maximum run depth was 1.8 m in summer and 1.0 m in October; maximum riffle depth was 1.7 m in summer and was less than 0.5 m in October (Figure 20). Depth frequency distributions were skewed towards the left (shallow) side for riffles and runs in summer. Pool depth frequencies were more evenly distributed and extended further to the right than run and riffle depth frequencies.

In Loggers Creek pools were the deepest habitat type followed by runs and riffles (Table 10), but the differences were not significant. Maximum depth was 1.5 m in pools, 0.9 m in runs and 0.6 m in riffles (Figure 21). Depth frequencies were more evenly distributed and extended further to the right in pools than in runs and riffles.

During October 1987, the ten habitat units surveyed had mean depths which were shallower than the same units in summer 1987 (Table 11, Figures 12, 14, 16, and 18). Differences in the mean depth were significant in all but two of the habitat units--Pools 1 and 2 in section 2 (Table 11). October run and riffle depth frequencies were skewed to the left more than in the summer; pool depths were still evenly distributed but did not extend as far to the right as in the summer (Figure 20).

Water velocity. - Water velocity was fastest in riffles and slowest in pools in each section and in the study area (Table 12). Differences in mean velocities were significant between pools, runs, and riffles for the study area as a whole (P<0.05) (Figure 19), and within sections 1, 2, 4, and 5 some of the differences were significant (P<0.05) (Figure 10). Mean stream section water velocities were not significantly different from each other. Velocities ranged from 0.0 to

Table 11. Mean widths, depths and velocities for habitat units measured during summer and October, 1987, in the Boise River. Boundary transects were included to calculate means. For each habitat unit n = 3. Vertical lines to the right of two values indicate no significant difference between the values (alpha = 0.05, paired t test).

Width (m) Depth (m) Velocity (m/s)

Section 1

Run 1 Summer 57.70 0.50 0.50 October 46.20 0.24 0.18

Run 2 Summer 49.40 0.54 0.44 October 42.80 0.33 0.17

Run 3 Summer 55.50 0.69 0.44 October 54.10 0.31 0.17

Pool 3 Summer 43.80 0.88 0.30 October 40.40 0.65 0.09

Riffle 1 Summer 32.831 0.40 0.77 October 30.20 0.16 0.35

Riffle 3 Summer 32.30 0.48 0.69 October 23.50 0.24 0.33

Section 2

Run 2 Summer 30.921 0.48 0.47 October 26.30 0.30 0.22

Run 4 Summer 29.101 0.49 0.421 October 24.20 0.34 0.27

Pool 1 Summer 43.101 0.751 0.26 October 34.30 0.74 0.09

Pool 2 Summer 38.601 0.711 0.311 October 30.70 0.56 0.19

Table 12. Mean habitat type depths (m), velocities (mjs), ranges (in parentheses), and number of measurements for Boise River sections and study area for 1986 and 1987 summer flow periods. Boundary transects were excluded when calculating means and ranges.

Pool Run Riffle

N Depth Velocity N Depth Velocity N Depth Velocity

Section 1 59 0.93 0.35 (0-3.05) 131 0.740.49 (0-1.86) 75 0.59 0.69 (0-1.75) (0-1.18) (0-1.39) (0-1.55)

Section 2 54 0.84 0.29 (0-2.22) 136 0.560.47 (0-1.81) 149 0.68 0.50 (0-1.13)

43 (0-1.28) (0-1.27) (0-1.51)

Section 3 38 0.92 0.36 (0-2.74) 143 0.630.48 (0-1.61) 37 0.24 0.51 (0-0.61) (0-1.00) (0-1.42) (0-1.58)

Section 4 51 0.56 0.11 (0-1.65) 44 0.420.20 (0-1.07) 24 0.18 0.42 (0-0.43) (0-0.37) (0-0.61) (0-1.07)

Section 5 84 0.57 0.14 (0-2.13) 63 0.320.19 (0-1.10) 37 0.18 0.62 (0-0.61) (0-0.61) (0-0.58) (0-1.95)

Study area 286 0.74 0.24 (0-3.05) 517 0.580.42 (0-1.86) 322 0.36 0.56 (0-1.75) (0-1.28) (0-1.42) (0-1.95)

1.2 m/s in pools, 0.0 to 1.45 m/s in runs and 0.0 to 1.9 m/s in riffles (Figure 22), but mean velocities and the frequency distribution of velocities are more indicative of the difference between pools, runs, and riffles. Pools had the largest amount'of slow water and riffles the least in summer and October. Water velocity tended to be slower towards the bank and bottom of the habitat units surveyed (Figures 12, 14, 16, and 23). The fastest water was in the middle of the channel and made up from 22 to 68% of the transect cross sectional area in the four habitat units presented graphically in which velocity was measured every one half foot (Table 13, Figures 12, 14, 16, and 23). The amount of slow water (< 0.20 m/s) varied between the four habitat units and between transects within habitat units with Pool 3 having the largest amount and Pool 2 the least.

In Loggers Creek, nearly 50% of the water velocities measured were from 0.0 to 0.09 m/s in runs and pools, versus about 37% in riffles (Figure 24). Mean riffle water velocities were faster than mean run and pool velocities (Table 10), but the differences were not significant because of the large variance. Riffle velocities ranged higher than those in runs and pools. Loggers Creek pool velocities ranged from 0.0 to 0.7 m/s, run velocities ranged from 0.0 to 0.8 m/s and riffle velocities ranged from 0.0 to 1.2 m/s.

Water velocities decreased from summer to October 1987 in the ten habitat units measured during both flow periods (Table 11, Figures 12, 14, 16, and 18). Differences between summer and October mean habitat unit velocities were significant for every unit except Run 4 and Pool 2 in section 2 (Table 11). In pools, runs, and riffles water velocity frequency distributions for October measurements were skewed to the left more than during summer months (Figure 22). Velocity frequency distributions of runs and pools were similar in October.

Water velocity taken at 0.6 total depth tended to overestimate mean water column (vertical) velocity (Figure 25). The differences generally increased further out in the channel and decreased near the banks. In most cases the two values were within 0.1 m/s of each other.

Substrate composition. - Cobble-sized rocks (63.5 to 254.0 mm in diameter) were the most abundant substrate in the Boise River followed by pebble (6.4 to 63.5 mm in diameter) and sand (less than 1.5 mm)(Figure 26). Substrate composition varied between study sections and habitat types (Figures 26 and 27). In sections 1, 2, and 5 cobbles were the most abundant substrate in all types of habitat. There was no clearly dominant substrate type in section 3, but sand, pebble and cobble were most abundant and similarly distributed among the habitat types. Pea gravel (1.5 to 6.4 mm in diameter) was more abundant in section 3 (especially in riffles) than in other study sections. Cobbles were the most abundant substrate in section 4, but pebbles were nearly as common in run type habitat units. In the five habitat units previously described for depth and velocity, substrate composition varied between units and between transects within units (Figure 28). Cobbles were most abundant in three of the units while pebbles were most abundant in Run 3, section 5, and pebble and sand was most abundant in Pool 3, section 1.

Table 13. Percent relative abundance of three water velocity classes presented graphically in Figures 12, 14, 16, and 25 for two pools and two runs in the Boise River. Water velocity was measured every 15.2 cm depth interval of each vertical during the summer of 1987.

Velocity class (m/s)

Study site Line < 0.20 0.20 - 0.40 > 0.40

Pool 3 1 42% 15% 43% 2 33% 8% 59% 3 25% 13% 62%

Pool 2 1 2% 71% 27% 2 35% 18% 47% 3 20% 20% 60%

Run 2 1 20% 12% 68% 2 29% 14% 57% 3 33% 5% 62%

Run 3 1 11% 67% 22% 2 30% 33% 37% 3 24% 20% 56%

In Loggers Creek the composition of the substrate was more evenly distributed among the six substrate types (Figure 27), with runs and pools having more silt and sand, and riffles having more cobble and pebble.

In the Boise River more than 60% of the pea gravel, pebble and cobble was embedded in the 25 to 49% range, with the remainder embedded in the 0 to 24% and 50 to 74% range (Figure 29). Boulders were generally free of sand and silt. In the five units presented graphically, the embeddedness of the substrate was similar to that in the Boise River as a whole (Figure 29).

Most of the pebble and cobble in Loggers Creek was embedded 0 to 24%, but most pea gravel was embedded 25 to 49% (Figure 29). Boulders were embedded at various classification ranges in Loggers Creek.

Cover. - In habitat units surveyed in the Boise River, 70% of the surface area had no cover elements for trout other than depth (Figure 30). Where cover was present, it was most frequently instream and a combination of instream and overhead cover. Sections 3 and 4 had more cover (56% and 48% of the cells, respectively) than the other sections (Figure 31); these were the narrowest sections so overhead cover extended further out over the channel. Instream and overhead cover were located predominantly near the banks. In the five habitat units previously described for depth and velocities (Figures 11-18 and 23),

lack of cover was particularly evident (Figure 32), with Pool 3, section 1, having more cover than the other four units.

In Loggers Creek the combination of instream and overhead cover was present in over 50% of the classifications (Figure 30). Instream cover alone was the next most abundant cover type followed by no cover and overhead cover.

Water temperature

Mean daily water temperatures increased during the summer and peaked in late August at the four upstream temperature recorder locations and in late June to early July at Star (Figure 33). Temperatures reached a low of 0 °C during January, 1987, at Barber Park and at Eagle Road in the North Channel. Temperature patterns at the five sites from Barber Park to. Star were similar, but temperatures were consistently lower at Barber Park than at downstream sites. Diel fluctuations varied between sites with the Barber Park site having the smallest daily range followed by the South Channel at Phylliss Canal, and then the other three sites (Figure 34). Daily temperature fluctuations were smaller in winter than in spring and summer. Cumulative temperature units (1 unit for each °C above 0 °C each day) were lowest at Barber Park, then increased downstream and were highest at Star (Figure 35).

Fish abundance

Mountain whitefish were caught at all 6 sites while electrofishing in October and were the most abundant salmonid (Table 14). We caught more whitefish above Glenwood Bridge (376) as compared to below (116); however, effort at the Linder Road site was less than effort at the other five sites. Brown trout collected with electrofishing gear ranged from 110-200 mm, hatchery rainbow trout 120-270 mm, wild rainbow trout 110-240 mm, and mountain whitefish 100-500 mm (Figure 36). Other fish species captured with electrofishing gear but not enumerated or measured included redside shiner, chiselmouth, sculpin, sucker, northern squawfish, and largemouth bass.

Of the salmonids counted while snorkeling, mountain whitefish were the most abundant in the Boise River and Loggers Creek during August 1986 (Table 15). We counted few rainbow trout in all the study sites snorkeled; brown trout were more abundant than rainbow trout and were all 160 mm or less in length. Mountain whitefish ranged from about 160 to 500 mm in length and rainbow trout 200 to 300 mm (lengths approximated visually).

Table 14. Number of salmonids collected by electrofishing from six sites in the Boise River on 25, 26, and 27 October, 1986 while flows were low (169 cfs at Barber Park and 145 cfs at Glenwood Bridge).

Hatchery Wild Mountain rainbow rainbow Brown Site whitefish trout trout trout

Barber Park 77 1 2 1

Municipal Park 144 1 1 5

Ann Morrison Park 155 0 5 1

Glenwood Bridge 67 0 6 15

Eagle Road (North Channel) 36 0 0 3

Linder Road (South Channel) 13 2 1 0

Totals 492 4 15 25

Table 15. Number of salmonids counted by snorkeling in Boise River and Loggers Creek study sites during August 1986. Mountain whitefish size classes were 0 to 100 mm (age 0), 101 to 200 mm (age 1), and > 200 mm (age 2+). Rainbow and brown trout size classes were 0 to 85 mm (age 0), 86 to 200 mm (age 1), and > 200 mm (age 2+).

Mountain whitefish Rainbow trout Brown trout

Stream Section Age groups Age groups Age groups Habitat unit 0 1 2+ 0 1 2+ 0 1 2+

Boise River Section 1 Run 1 0 6 101 0 0 3 48 8 0 Riffle 1 0 2 55 0 0 0 0 16 0 Section 2 Run 1 0 0 106 0 0 0 12 4 0 Riffle 1 0 24 80 0 0 0 11 1 0

Loggers Creek Pool 1 0 0 1 0 0 0 0 0 0 Pool 2 0 0 0 0 0 0 0 1 0 Pool 3 0 0 0 0 1 0 0 0 0 Pool 4 0 6 3 0 1 0 0 0 0 Riffle 1 0 0 0 0 1 0 0 1 0 Riffle 2 0 0 0 0 0 0 0 0 0 Riffle 3 0 3 1 0 0 0 0 0 0 Riffle 4 0 3 3 0 0 0 0 0 0 Run 1 0 4 2 0 0 0 0 0 0 Run 2 0 0 0 0 0 0 0 0 0

Anglers returned 120 tags from the 986 tagged rainbow trout released in the Boise River in 1986. One hundred and seven of the tagged trout were caught at the release location. Of the remaining 13 trout, ten were caught within 0.5 km of the release point, one 1.6 km upstream, one 2.5 km upstream, and one 12.7 km downstream. Most of the fish (74%) were caught within two months of release; 5 trout were caught in January 1987, and two in May 1987.

DISCUSSION

In summer, the Boise River is not ideally suited to trout because velocities are too high in the upper sections and temperatures are too high in the lower sections. Of the physical habitat parameters we measured in the Boise River, the three that were most likely to affect trout abundance were summer water velocities, summer temperatures, and winter cover.

Water velocity is an important physical parameter affecting position choice of trout in streams (Baldes and Vincent 1969). Allopatric and sympatric (with rainbow trout) brown trout in six diverse New Zealand rivers chose specific, but separate, feeding and spawning microhabitats, and velocity appeared to be the most important factor determining position choice (Shirvell and Dungey 1983). They noted that brown trout chose positions with optimum combinations of depth and velocity, not positions with optimum values for either variable alone. Lewis (1969) found current velocity to be the most important physical variable for habitat selection by rainbow trout. Binns and Eiserman (1979) also found velocity to be an important variable in the model they used to predict trout biomass in Wyoming streams. Areas with unsuitable velocities for different trout life stages are not likely to contain trout, even if there is abundant food and cover. Juvenile trout and salmon (< 120 mm in length) in streams usually select focal point velocities less than or equal to 0.20 m/s during the summer (Everest and Chapman 1972; Smith and Li 1983; Moyle and Baltz 1985; Sheppard and Johnson 1985; Hillman et al. 1987). Water velocities in habitat units in the upper sections of the Boise River during summer were higher than 0.20 m/s except near the banks and bottom of the channel (Figure 8). If the focal point velocities selected by juvenile trout are close to the maximum they can handle on a sustained basis, young trout in the Boise River would be limited to areas near the bank or close to the bottom.

Trout larger than 120 mm are typically found in velocities at or below 0.40 m/s (Horton and Cochnauer 1978; Shirvell and Dungey 1983; Moyle and Baltz 1985). Larger fish could use more of the river than juveniles from a velocity standpoint, but much of each habitat unit in the upper sections of the Boise River was still unsuitable because velocities exceeded 0.40 m/s. In sections 1, 2 and 3 during summer, runs were the most abundant habitat type and they had velocity profiles similar to that in run 2, section 1 (Figure 8). Velocities likely did not limit trout in sections 4 and 5 because velocities were slower (Table 5) and pools were most abundant (Figure 3).

Mountain whitefish were more abundant that trout in habitat units snorkeled and electrofished (Tables 6 and 7). Horton and Cochnauer (1978) sampled mountain whitefish in addition to trout in five Idaho rivers in an attempt to determine depth and velocity preferences. Most whitefish they caught were longer than 203 mm and they were found in areas with 0.6 depth velocities that ranged from 0 to 1.2 m/s (mean = 0.53 m/s). Since they measured velocity at 0.6 of total depth at the point of capture and not at the fish's focal point, the velocities

reported may not reflect velocities used by whitefish. While snorkeling in the Boise River, 'I observed whitefish on or near the bottom where velocities were slower than velocities at 0.6 depth. Mountain whitefish typically live closer to the stream bottom and are thereby able to use habitat with faster mean water column velocities than trout.

Water velocities in the Boise River after the irrigation season were slower than in summer (Table 4) and more suitable for salmonids. Salmonids choose sites with slower water velocities when temperatures decrease (Rimmer and Paim 1984; Hillman et al. 1987). Allen (1969) noted that in winter in temperate climates, all stream dwelling salmonids move to pools and seek cover. Many habitat units classified as runs in the summer were classified as pools in winter (Figure 3), particularly upstream from Eagle Island. Slower water velocities in all habitat types and a greater abundance of pool habitat would benefit trout in the Boise River in winter.

Water temperatures increased downstream from Barber Park (site 1) during the summer (Figure 11) and in late summer and early fall were above temperatures because most of the food intake is used for body maintenance. Bowlby and Roff (1986) state that maximum summer stream temperature may be the most universal variable limiting trout in streams and found mean maximum summer stream temperatures to be important in predicting trout biomass in Ontario. Brown trout growth rates declined under experimental conditions at temperatures above 12 to 15°C despite abundant food (Elliott 1975). Hokanson et al. (1977) found rainbow trout fed to satiation exhibited increased growth rates with increasing temperature up to 170C (constant temperature) and 15°C (diel fluctuating temperature, ± 3.8°C), but growth rates then declined as temperatures were increased further. Summer diet daily temperatures below Glenwood Bridge (site 2) often fluctuated above 16°C for an extended period each summer (Figure 12). Deep water releases from Lucky Peak Reservoir reduced diel fluctuations and the maximum summer temperature in the upper sections of the study area, as has been observed on the River Tees, England (Crisp 1977), and the Rogue River, Oregon (Smith and McPherson 1981).

Despite warm temperatures in the late summer and early fall, the Boise River may still be able to produce large healthy trout. Holubetz (1988) found that naturally produced trout captured by electrofishing were in excellent body condition as indicated by the ratio of weight to length. In upper Colorado River tailwaters trout growth varied but was generally good (76 - 380 mm per year), even in the two tailwaters where mean monthly temperatures approached 29°C in late summer and early fall (Mullan et al. 1976). In fact, most cold tailwaters can be termed put- grow-and-take fisheries because growth is generally good for stocked trout below impoundments (Pfitzer 1975; Wiley and Mullan 1975). Tailwaters below reservoirs with releases from near the bottom, as is the case in the Boise River, benefit trout because the reservoir acts as a heat trap and nutrient exporter (Mullan et al. 1976). The release of nutrient-rich water into tailwaters stimulates primary production, ultimately increasing the amount of food available for trout. Increased food production would benefit trout in the Boise River

because as the temperature increases so does standard metabolism and food demand (Smith and Li 1983).

Cover (instream and overhead), when present in the Boise River, was located close to the banks. Cover serves as a means of predator avoidance, and in streams may provide areas of moderated current speed for fish (Giger 1973). While snorkeling in the Boise River we observed most rainbow and brown trout close to the bank in association with something that provided a velocity break, usually instream woody debris or rocks. Mountain whitefish were in the main channel and always close to the bottom. Lewis (1969) found cover to be the most important variable to brown trout densities irrespective of current velocity. It was unusual to find brown trout in the Boise River that were not associated with instream woody debris or rocks. Much of the river, especially in the middle of the channel, lacked large roughness elements (i.e. boulders, logs) that can provide diversity of channel form (Lisle 1981) and velocity shelters for salmonids. Without such cover elements in the middle of the channel a large portion of the habitat will remain unsuitable and unused by trout. Undercut banks can be important hiding places for salmonids (Jenkins 1969; Brusven et al. 1986) but were lacking in the areas we snorkeled and surveyed. When undercut banks were present, we rarely saw trout associated with them, perhaps because velocities were fast in those areas.

Despite the increased amount of low velocity water in which to live in winter, the low frequency of cover elements may hinder winter survival of trout. During winter, many of the pools in the Boise River are long and shallow and may not provide enough cover for trout. Cover losses occur with lowered flows when water pulls away from the bank (Wesche 1978). Vegetation along the Boise River was keyed to the summer flow boundary and was often some distance from the winter flow boundary.

Interstitial spaces between large rocks are important to over- wintering salmonids (Chapman and Bjornn 1969; Bjornn et al. 1977). Though large cobble substrate was abundant in the Boise River, most of it was embedded 25 to 49% with fines, reducing the number of usable winter hiding places.

Most of the Boise River streambed was armored with cobbles (Figure 9), and spawning sized gravel (pea gravel and pebble) was not abundant. Reservoirs act as sediment traps (Mullan et al. 1976) and halt recruitment of sediments from upstream sources. Even when gravel suitable for spawning was present, it was usually embedded 25 to 49% with fines (Figure 9). Bjornn et al. (1977) found that the survival and emergence of salmonid embryos declined when the percentage of fine sediment exceeded 20 to 30%. Without adequate spawning habitat it is improbable that rainbow and brown trout will produce large natural populations.

Angler harvest is another factor which could be limiting trout abundance in the Boise River. Estimated angler harvest of stocked rainbow trout in the river from RK 93.6 to 76.4 was 81% from March 1, 1986 to January 2, 1987 (Reid and Mabbott 1987). If the exploitation

rate for wild rainbow trout living in the river upstream from RK 76.4 and near the heavily fished access points downstream from RK 76.4 approached 80%, the combined fishing plus natural mortality rates would be high enough to prevent wild rainbow trout from becoming abundant. Holubetz (1988) found the largest numbers of wild rainbow trout in the South Channel around Eagle Island. The South Channel has limited access for anglers and some of the best habitat, in terms of cover, for trout. Brown trout made up a small portion of the harvest from the Boise River (Reid and Mabbott 1987) and were also not abundant in our electrofishing samples or snorkel observations, nor were they abundant in electrofishing samples conducted by the IDFG (Holubetz 1988). The fact that brown trout were not more abundant and of a small size indicates that physical habitat factors, combined with angler harvest, are probably limiting the abundance of trout in the Boise River.

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