INVENTORY AND SURVEY OF SELECTED STREAM FISHERIES OF THE RED ROCK, RUBY, AND BEAVERHEAD RIVER DRAINAGES OF SOUTHWEST MONTANA; 2003 - 2006 By: Richard A. Oswald October 2006 Montana Department of Fish, Wildlife & Parks Region Three 1400 S. 19th Avenue Bozeman, Montana ABSTRACT Trout population data are presented for six study sections on the Beaverhead River. Trout populations of the upper river tailwater environment declined substantially in association with drought influenced declines in flow below the recommended minimum of 200 cfs. Brown trout populations suffered declines in density, standing crop, numbers of older, larger fish, and condition similar to those experienced in prior drought episodes of the late 1980's and early 1990's. Lower river brown trout and mountain whitefish populations also exhibited substantial declines in association with low flow regimes. Salmonid population data are presented for two study sections in the upper Ruby River. Trout populations declined substantially from drought influenced flows exhibiting reductions in density, standing crop, recruitment, and condition factor. Data are also presented describing Arctic grayling reintroduction efforts in the upper Ruby River. Trout population data are presented for two study sections sampled in the lower Ruby River system. The affects of the recent drought on brown trout populations are discussed among the various study sections over the period of record. The trout populations of Poindexter Slough are presented for the study period. Brown trout population declines and recovery are discussed in regard to flow reductions in the system. Brown trout population data for a new study section on the Red Rock River are presented and data compared with similar study sections that were sampled in the late 1980’s and early 1990’s. 2 ACKNOWLEDGMENTS The author would like to gratefully acknowledge the able assistance of the following individuals in the collection of field data under often arduous conditions; Scott Lula, Tim Mosolf, Jon Hoerning, Tracy Elam, Sam Hochhalter, James Magee, Austin McCollough, Adam Petersen, and Emily Rens. The author would also like to thank Dick Vincent, Jim Peterson, Ken Staigmiller, Jeff Bagdanov and Jody Hupka for assistance in the analyses of Whirling Disease samples. Finally, the author would like to acknowledge the assistance of Bob McFarland, Reed Simonson, Wayne Black, and Deanna Meredith in data preparation and analysis techniques. 3 TABLE OF CONTENTS Page INTRODUCTION..............................................................................................................…. 1 METHODS.........................................................................................................................…. 4 RESULTS...........................................................................................................................…. 5 UPPER BEAVERHEAD RIVER STUDY SECTIONS.............................................. 5 LOWER BEAVERHEAD RIVER STUDY SECTIONS............................................. 7 UPPER RUBY RIVER STUDY SECTIONS............................................................. 11 LOWER RUBY RIVER STUDY SECTIONS........................................................... 15 POINDEXTER SLOUGH STUDY SECTION.......................................................... 17 RED ROCK RIVER STUDY SECTIONS................................................................ 18 DISCUSSION.....................................................................................................................… 20 UPPER BEAVERHEAD RIVER STUDY SECTIONS.............................................. 20 LOWER BEAVERHEAD RIVER STUDY SECTIONS............................................ 22 UPPER RUBY RIVER STUDY SECTIONS............................................................ 23 LOWER RUBY RIVER STUDY SECTIONS........................................................... 24 POINDEXTER SLOUGH STUDY SECTION.......................................................... 25 BIG SHEEP CREEK STUDY SECTIONS................................................................ 26 LITERATURE CITED.......................................................................................................... 28 APPENDIX OF FIGURES.................................................................................................... 31 4 INTRODUCTION The mainstem river fisheries of the upper Missouri River drainage of southwest Montana are nationally renowned for their wild trout populations and “blue ribbon” fisheries. These river systems, first described by the Lewis and Clark expedition in the early 1800’s, also contain smaller tributary streams which provide high quality sport fisheries or support native fish populations in isolated settings. The popular sport fisheries of these drainages are based on abundant wild trout populations and support relatively high angler use, both of which have recently undergone relatively substantial declines associated with severe drought conditions (Oswald 2003, 2004, 2005). Similar declines in trout populations and angling pressure were observed in the drought episode of the late 1980's and early 1990's. More recent precipitation and snowpack conditions have resulted in improvements in soil moisture and surface water supply, warranting a drought –free classification for Beaverhead and Madison counties in 2005 (NRCS and NWS classification data 2005). Depleted aquifers and reservoir storage pools resulting from 5 to 6 years of continuous drought have maintained reduced flows in most area streams throughout the report period, however. This report details wild trout and mountain whitefish population dynamics in selected study sections of mainstem rivers and tributary streams in the Red Rock, Ruby, and Beaverhead River drainages of southwest Montana which were last described by Oswald (2003). The streams of southwest Montana support a relatively limited diversity of native fish species to include westslope cutthroat trout; Arctic grayling; mountain whitefish; burbot; white, longnose, and mountain sucker; longnose dace, and mottled sculpin. Concern over the future of native fluvial Arctic grayling of the upper Missouri River system has led to recent grayling reintroduction projects beginning in 1997 in the upper Ruby River and in 1999 in the lower Beaverhead River (Oswald, 2000c). Concern over the future persistence of native westslope cutthroat trout has resulted in numerous studies of population genetics and hybridization, competition with introduced species, and habitat limitations. These studies have resulted in recent projects which have attempted to improve habitat quality, reduce competitive factors and expand westslope cutthroat trout distribution within the upper Missouri drainage (Oswald 1999, 2000c, and 2003). The popular sport fisheries of southwest Montana are largely based upon wild populations of introduced salmonids including the brown, rainbow, and brook trout as well as lesser tributary contributions of Yellowstone cutthroat trout or rainbow trout and their hybrids with native westslope cutthroat trout. Introduced nongame species include the red side shiner minnow and common carp which are present at low density in lower reaches of the mainstem river systems. The Beaverhead River supports variable populations of brown and rainbow trout dependant upon dominant habitat type, regulated flow regimes, inverted lower river hydrograph, distance from the tailwater of Clark Canyon Dam, sediment loading, thermal regime, and riparian development. The Beaverhead River can be roughly bisected into upper and lower river reaches at the City of Dillon, Montana based on flow regime. The upper river reach generally depends upon irrigation and flood control releases from Clark Canyon Dam for its dominant flow regime that can result in an extremely productive “tailwater” reach between the dam and Barretts Diversion. A spring runoff component can be introduced in the reach from major tributaries such as Grasshopper and Blacktail Deer Creeks which can also augment base flow. Summer stream flows generally remain ample while winter flows can often exhibit critical low flows for the maintenance of fish habitat. The lower river reach exhibits an inverted hydrograph in which 5 spring and summer flows are often minimal and winter months are characterized by a rising hydrograph as irrigation water drains from alluvial terrace formations surrounding the valley floor. Lower river tributaries are largely representative of valley floor spring creeks or “sloughs” and are subject to the same inverted hydrograph as the river. The sport fishery of the Beaverhead River is dominated by brown trout while limited rainbow trout populations have been supported between Clark Canyon Dam and the city of Dillon, Montana. Beginning in 1999, an attempt was made to reestablish an Arctic grayling population in the lower river between the mouth of Stodden Slough and the confluence of the Beaverhead and Big Hole Rivers. This introduction effort was postponed after the 2001 plant due to persistent low summer flows and high water temperatures associated with drought conditions and low flow release regimes from Clark Canyon Dam. Past angler use of the Beaverhead River has been concentrated in the upper tailwater portions of the system between Clark Canyon Dam and Barretts Diversion. This concentrated use pattern has persisted to the present but estimated pressure had increased from 15,093 angler days in 1991 to 39,726 angler days in 1997 and 39,622 in 1999 (MFWP 1989- 2001) with nonresident angler use accounting for about 63% of the total angler user days. In 2001, the Montana Fish Wildlife and Parks Commission established a Biennial Rule regulation that restricted float fishing use by commercial outfitters and nonresident anglers. This rule was renewed by the Commission for another two year period in 2003 and extended again in 2005. Angling pressure in 2001 declined markedly to an estimated 14,574 angler days, however, the percent contribution of the nonresident angler component remained high at 62.2% of the total. The 2001 pressure was similar to that observed in the drought influenced 1991 estimate and declines were similar to those observed in other area rivers which suffered drought influenced flow regimes. Angling pressure rebounded to 26,968 angler days in 2003 despite continuing low flow conditions, however, the nonresident component increased to 70.8% of the total. Angler use in 2005 declined back to 22,069 angler days with 55% nonresident participation as low stream flows and declining fish populations persisted. Oswald (2003) last described the salmonid populations of the Beaverhead River. The fisheries of the Ruby River can be examined as two systems also, i.e., a lower river and an upper river environment, roughly bisected by the Ruby Reservoir. The lower Ruby River supports relatively abundant populations of brown trout in habitats downstream from the Ruby Reservoir. The size composition and abundance of these populations is dependant upon distance from the reservoir tailwater, dominant habitat type and condition, and flow release regime from the dam. Oswald (2000c) presented a relatively complete picture of brown trout density and production throughout the length of the lower Ruby River. Upper Ruby River fisheries are dominated by brown and rainbow trout in relatively close proximity to the reservoir while upper reaches of the river are dominated by a hybridized swarm of rainbow trout and westslope cutthroat trout. Since 1997, attempts have been made to reintroduce a fluvial Arctic grayling population in the upper Ruby River. In 1994, a complete dewatering of Ruby Reservoir occurred (Oswald 2000a and 2000c) resulting in a significant fish kill in a limited reach of the Ruby River tailwater downstream from the dam. This event led to the formation of a Governor’s Ruby River Task Force that investigated and recommended methods to promote adequate storage in Ruby Reservoir and adequate flow regimes for irrigation and fisheries in the Ruby River. Oswald (2000c and 2003) described the response of the fisheries to abundant flow regimes of the late 1990’s followed by the reduced flows of the current drought episode. In 1995, angler frustration over decreasing access to private lands along the lower Ruby River led to the formation of a Governor’s Ruby River Fishing Access Task Force. Recommendations of this Task Force led to 6 the formation of a Lower Ruby River Fishing Access Plan (MFWP 1996) and the ultimate acquisition of 5 public fishing access sites along the lower river corridor in 1996. Increased public access had an immediate affect on angling pressure within the lower Ruby River reach. In 1997, angling pressure on the lower Ruby was estimated at 9,458 angler days, a marked increase over the 1995 pressure estimate of 5,974 angler days (MFWP 1989-2001). Angling pressure continued to increase to an observed high of 13,996 angler days in 1999 but declined markedly to 9,162 in 2001. Similar to the Beaverhead River, nonresident anglers composed 62.6% and 64% of the 1999 and 2001 angling pressure, respectively. The 2003 and 2005 pressure estimates exhibited an increase in angler use to 11,317 and 11,356 angler days with nonresident use composing 57% and 55% of the total pressure, respectively. Angling pressure in the upper Ruby River has historically remained relatively low despite an abundance of public ownership on Beaverhead National Forest lands. Pressure estimates from 1989 through 1995 averaged 685 angler days per year with an observed maximum of 862 in 1991. Similar to trends in other area rivers, angling pressure increased sharply to 1,591 and 1,252 angler days in 1997 and 1999 but declined under the influence of drought impacted flows to 763 angler days in 2001 and rebounded markedly to 2,020 angler days in 2003. The 2003 angling use was dominated by resident fishermen at 62.7% of the use. The 2005 pressure estimate of 1,684 angler days was quite comparable to the modern pre-drought use levels of 1997 and 1999. The 2003 and 2005 pressure estimates were probably reflective of improved summer flow regimes in both of those sample years. Fish population data for both the upper and lower reaches of the Ruby River were last reported by Oswald (2003). Poindexter Slough is a major public spring creek fisheries resource. It is tributary to the Beaverhead River and is located in close proximity to the city of Dillon, Montana. While base flows of Poindexter Slough are maintained through accretions from numerous valley floor spring sources, a significant portion of the stream’s summer flow consists of irrigation water diverted from the Beaverhead River. The fishery of Poindexter Slough is dominated by wild brown trout which attain extremely high density due to an abundance of favorable spawning and rearing habitat. Much of the productive fisheries reach of Poindexter Slough is located on public fishing access property maintained by MFWP. Recent angling pressure estimates indicate a use rate of approximately 3,000 angler days per year through 1999 (MFWP 1989 - 2001). Unlike most other area waters, Poindexter Slough has maintained a relatively stable base flow from spring sources despite severe drought conditions. As a result, angling pressure increased in 2001 to an observed high of 4,095 angler days. Recent restrictions in river water diverted into the Slough, however, have resulted in diminished flow regimes and declining angler use down to 2,757 angler days in 2003 and 1,589 angler days in 2005.The brown trout populations of Poindexter Slough were last described by Oswald (2003). The Red Rock River is representative of another system bifurcated by an irrigation dam and reservoir. The river originates in the upper Centennial Valley of southwest Montana as the geographic origin of the Missouri River system at Hell Roaring Creek. The upper river supports sparse fisheries between Red Rock lakes and Lima Reservoir due to limited habitat niche diversity and abundance associated with relatively low gradient in a sand dune, ancient lake bed geology. The 57.4 mile lower river reach between Lima and Clark Canyon Reservoirs can support relatively abundant gamefish populations of wild brown trout and mountain whitefish as well as limited populations of rainbow trout. The lower river reach also provides important spawning habitat for adfluvial rainbow trout, brown trout, and mountain whitefish from Clark Canyon Reservoir on a seasonal basis (Oswald 2004). A new study section was initiated in the 7 Red Rock River near the town of Dell, Montana in 2005. The Martinell Section was selected to monitor brown trout populations in the aftermath of severe drought conditions, angling closures, and voluntary efforts by landowners to maintain minimal stream flow. The Martinell Section originates upstream from the confluence with Big Sheep Creek and terminates at the channel bifurcation upstream from the Sage Creek Road. The section is 4,518 feet in length. The resident trout populations of the Red Rock River near Dell, MT were monitored briefly during the drought episode of the late 1980’s and early 1990’s (Vincent et al 1990) in the aftermath of a total dewatering of the channel that persisted for 10 months between July 1988 and May 1989. These earlier efforts were concentrated in the Wellborn and Dell Study Sections located adjacent to each other immediately downstream from the current Martinell Section. Reaches up and downstream from the Martinell Section were observed as totally dewatered or carrying minimal flows of 1. 0 to 4.0 cfs at different base summer flow regimes during the current drought episode. The Martinell Section, however, maintained minimum base flows in the 25 to 30 cfs range throughout the same period. The Red Rock River usually supports a relatively low angler use due to a preponderance of private land ownership and limited opportunities for public access. From 1991 through 1999 angling pressure on the Red Rock River averaged 1,277 angler days per year, peaking, similar to other area waters, in 1997 at 2,375 angler days. Fishing pressure on the Red Rock River has been heavily dominated by nonresident use averaging 77.8% over the 1991 – 1999 survey period. Recent voluntary and mandatory drought based fishing closures placed within the system from 2000 through 2004 had severely reduced or virtually eliminated angler use within the Lima Dam to Clark Canyon Reservoir reach. The opportunity to fish the river in 2005 did not result in a return to pre-drought use levels with an estimated 514 angler days expended in the reach. METHODS Trout populations in rivers and large streams were sampled through the use of electrofishing techniques based on mark-recapture methodologies described by Vincent (1971). Electrofishing was conducted via boat mounted, mobile anode techniques which utilize a 3500 watt generator and Leach type rectifying box. A straight or continuous wave DC current is used at 1,000 to 1,800 watts. Fish captured within the field were drawn to the boat, netted, and deposited into a live car. Boats consisted of a modified Clackacraft drift boat or modified Coleman Crawdad boat depending upon stream size. Individual fish captured were anesthetized, segregated by species, measured for length and weight, marked with a small identifying fin clip, and released. Scale samples for age determination were collected from a representative subsample by length. A single Marking run was made through each study section followed by a single Recapture run approximately 12 to 14 days later. Trout population statistics were analyzed under a log-likelihood methodology developed and described by Montana Fish, Wildlife and Parks (1994) under guidelines presented by Brittain, Lere, and McFarland (1998). Population estimates were largely calculated for brown trout from March and April samples collected from the study sections while rainbow trout, cutthroat trout, and Arctic grayling population estimates were calculated from September and October samples. The seasonal segregation by species was applied to avoid population estimate bias due to spawning movements and migrations. 8 RESULTS UPPER BEAVERHEAD RIVER Flow Regime Persistent drought conditions and resultant low storage pools have dominated the past five years in Clark Canyon Reservoir (Figure 1). Storage improved slightly in 2005 but did not result in any subsequent flow improvements in the Beaverhead River and did not attain the minimum recommended storage pool for fisheries last approximated in 2000. The current storage situation is similar to that experienced during the 1989 - 1992 period which resulted in extremely low over winter flow releases into the Beaverhead River and subsequent losses in trout populations (Oswald 1990, Oswald and Brammer 1993, Oswald 2003). Figure 2 demonstrates the affects of low overwinter dam releases on flows in the upper Beaverhead River and compares those flows with the Minimum Recommended Instream Flow (MFWP 1989) for the reach. Despite the appearance of relatively ample reservoir storage over most of the period, overwinter flows in the upper Beaverhead River have dropped below the recommended minimum in 16 of the 25 years depicted. In most of those years, flow dropped substantially below the recommended minimum resulting in significantly reduced wetted perimeter and substantial reductions in fish habitat availability and niche diversity. In the 2003 through 2006 water years, flow releases averaged only 27 cfs. In each of those years, flow reductions occurred in early September and did not improve until mid to late May. Flow accretions throughout the system improved flows as distance downstream from the dam increased but were insufficient to increase flow to the recommended minimum between the dam and the City of Dillon in any year since 2002. The extremely low overwinter flow regimes have represented only about 13.5% of the recommended instream flow for fisheries and aquatic habitat maintenance and have become a chronic situation over the past six water years. Hildreth Study Section Brown trout population density and standing crop are presented in Figure 3 for the 1986 through 2006 period. Brown trout density and, particularly standing crop, have declined with low winter flow regimes over the 2000 - 2006 period. While brown trout population density declined from the observed highs which exceeded 2,100 Age II and older fish per mile in 1998 and 1999, it remained relatively stable in the succeeding years through 2005. Brown trout standing crop, however, has declined in a steep, linear fashion throughout the 2000 - 2006 period to an observed modern low in 2006. Brown trout density also declined to roughly equal modern observed lows in 2006. While declines in standing crop were steep and sharply defined through 2005, the 2006 estimate represented a decline in biomass of more than 2,000 pounds per mile from highs observed in 1999. The steep declines in brown trout biomass were correlated directly with substantial losses in numbers of older, larger fish. Numbers of 18 inch and larger brown trout (Figure 4) soared to 832 per mile in 1999 following ample flow regimes (Figure 2) but had declined, in a steep linear fashion, to 296 per mile by 2005 and 102 per mile in 2006. Similar observations can be made, in more dramatic fashion, for 20 inch and larger brown trout (Figure 5) which largely compose the Age V and older segment of the population. During the low winter 9 flow regimes of the 1988 - 1991 and 1999 - 2006 periods record high numbers of these older larger fish declined markedly in a very linear fashion. Observed highs for these large fish occurred in 1988 and 1999 following periods of abundant flow. The 2006 estimate of only 9 twenty inch and larger fish per mile was the lowest density recorded in the sampling history of the study section. Densities of 22 inch and larger brown trout (Figure 6) continued to remain very low throughout the reporting period. Low numbers of larger brown trout can be correlated directly with steep declines in brown trout standing crop over the 2000 – 2006 period. Figures 7 and 8 clearly depict a situation under which the contribution of 18 inch and larger brown trout to the total Age II and older population has declined substantially to a modern low while numbers of 20 inch and larger brown trout have similarly declined as a segment of the 18 inch and larger segment of the population. Brown trout Condition Factor (K) over the recent period of declining stream flow is depicted in Figure 9. Mean population Condition for Age II and older brown trout declined in a linear fashion over the four year period through 2002 to a relatively low value of 32.35 for the upper Beaverhead River tailwater. As brown trout standing crop declined over the 2003 – 2006 period, mean brown trout condition recovered slightly but did not recover to numbers observed in 1999 or even 2000 under better flow regimes and much higher densities and standing crops. Condition for 18 inch and larger and 20 inch and larger fish declined more steeply and more severely, with increased length and age through the 2002 sample but similarly, improved through 2006 with markedly reduced density and standing crop of these larger fish. Similar to the overall population Condition Factor, recovered K values for the larger fish remained below those observed in 1999 and 2000. Similar relationships between overwinter flow and brown trout Condition Factor were depicted under the low overwinter flow regimes of the 1988 - 1990 period in the upper Beaverhead River by Oswald (1990) and Oswald and Brammer (1993), for the 1999 – 2000 period in the upper Beaverhead and Ruby Rivers (Oswald 2003) and over the 2000 – 2003 period in the Big Hole River (Oswald 2005). Trends in rainbow trout density and standing crop were last reported for the 1986 – 2000 period by Oswald 2003. Due to extremely low fall flow release from Clark Canyon Dam, rainbow trout population estimates were not conducted over the 2001 – 2005 period. Rainbow trout population sampling will be resumed when fall flow regimes improve in a significant manner. Pipe Organ Study Section Brown trout population trends are presented in Figure 10 for the 1986-2006 period of study in the Pipe Organ Section. Brown trout density and standing crop declined from an observed high of 1999 with low flow regimes experienced in the 2000 - 2006 period. Unlike the situation in the Hildreth Section, the decline in standing crop has not been linear and appeared to level out at about 1,000 pounds per mile over the 2004 – 2006 period. Brown trout density had experienced a linear decline following relatively good recruitment of Age II fish in 2001 (Oswald 2003) and declined to an observed low of about 1,000 fish per mile in 2005. Brown trout density increased slightly in 2006, however most of the increase was due to a large recruitment of Age II fish which was not accompanied by any significant increase in standing crop. Numbers of Age II brown trout in 2006 were estimated at slightly more than 700 fish per mile accounting for 56.6% of the total population. Numbers of larger brown trout (Figure 11), which had declined in a steep linear fashion from 1999 to 2002 (Oswald 2003), continued to decline to minimal densities in 2005 and 2006. Numbers of these 18 inch and larger fish dropped 10