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4 Current and Historical Status of River and Stream Ecosystems Aquatic ecosystems of the Klamath River basin have been extensively mocTifiecT by human activities that have changed hycTrology ancT channel morphology, increased fluxes of nutrients, increased erosion, introclucecT exotic species, ancT changed water temperatures. Efforts at restoration of cleclining native species neecT to recognize the unique characteristics of vari- ous portions of the basin in the current context of lancT use ancT human activities. This chapter considers the major streams ancT rivers of the Kla- math basin ancT analyzes anthropogenic changes in conditions that affect especially the coho salmon ancT enciangerecT suckers but also other fishes ancT aquatic life generally. Each section of this chapter considers either a specific section of the main-stem Klamath River or of its tributaries; loca- tions are clesignatecT in river mi (RM) from the ocean. TRIBUTARIES TO UPPER KLAMATH LAKE (RM 337-270) Streams ancT rivers above Upper Klamath Lake are a source of nutrients to the lake ancT provide spawning ancT larval habitat for enciangerecT suck- ers. The main sources of surface water for Upper Klamath Lake are the Williamson, Sprague, ancT WoocT rivers (Kane ancT Walker 2001; Chapter 21. Grounc~water ancT cTirect precipitation account for most of the balance of inflow. For Upper Klamath Lake, external loacTing of phosphorus, a key nutri- ent that promotes algal blooms (Chapter 3), comes primarily from the Williamson, Sprague, ancT WoocT drainages. Geologic features of this region 144

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 145 BEW ~ _ ~ ~ ~5 - - god ~L, no - \ FIGURE 4-1 Relative external phosphorus loading from tributaries and other sources to Upper I(lamath Lake. Source: Data from I(ann and Walker 2001. cause its streams ancT rivers to carry naturally high phosphorus loacTs (Chap- ter 31. Background concentrations of phosphorus, however, are augmented by human activity relatecT to lancT use ancT river modifications. The William- son ancT Sprague watersheds contribute 86 metric tons of phosphorus to Upper I(lamath Lake per year (I(ann ancT Walker 20011. The Williamson accounts for 21% of the total loacT, ancT the Sprague accounts for 27% (Figure 4-11. Recent changes in hycTrology may have affected total nutrient loacTing of Upper I(lamath Lake. Annual runoff from the Williamson ancT Sprague drainages increased from the period 1922-1950 to the period 1951-1996 (Risley ancT Laenen 19991. The cause of the change is uncertain, but it is inclepenclent of climatic variability ancT probably is relatecT to a combination of river channelization, reduction in area of wetiancTs, timber harvest, ancT other factors that recluce evapotranspiration in the watershed (Risley ancT Laenen 19991. Increased flows from the Williamson ancT Sprague drainages, couplecT with current lancT-use practices, probably have increased phospho- rus transport within the basin through greater erosion that leacTs to higher transport of suspenclecT sediments, which carry phosphorus. Estimates of sedimentation rates from cores taken in Upper I(lamath Lake support the hypothesis that transport of sediments from the watershed has increased in recent clecacles (Eilers et al. 20011. Although its watershed is much smaller than that of the Williamson River, the WoocT River is an important phosphorus source ancT has a high export of phosphorus per unit area of watershed (Figure 4-11. The balance

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146 FISHES IN THE KLAMATH RIVER BASIN of the phosphorus loacI to Upper I(lamath Lake comes from Seven Mile Creek, agricultural pumps, ancI miscellaneous sources. Virtually all of this phosphorus is from nonpoint sources, inclucling both natural ancI anthro- pogenic components. Rivers ancI streams above Upper I(lamath Lake support populations of coicI-water fishes, inclucling I(lamath recibancI ancI bull trout (Chapter 51. During summer, temperatures can be unclesirably high for these fishes in many stream reaches. For example, one threshoicI temperature that is used by government agencies to assess suitable rearing habitat for coicI-water fishes is 17.8C. The Williamson ancI especially the Sprague cluring late summer exceed this temperature (BoycI et al. 20011. In aciclition, concentra- tions of clissolvecI oxygen in the main stem of the Sprague River (mouth to junction of the North ancI South Forks) fall below Environmental Protec- tion Agency water-quality targets (BoycI et al. 20021. Mocleling indicates that restoration of riparian vegetation potentially couicI recluce tempera- tures in the Sprague through shacling (BoycI et al. 2002), ancI also couicI have a beneficial effect on oxygen concentrations because water hoicis more clissolvecI oxygen at low temperatures than at high temperatures. In acicli- tion, shacling couicI recluce the accumulation of algae ancI rooted aquatic plants on the sicles ancI becis of tributaries. Plants produce oxygen through photosynthesis ancI thereby potentially increased concentrations of clissolvecI oxygen cluring the clay, but nocturnal respiration ancI the clegraciation of accumulations of nonliving organic matter that they produce can cause oxygen clepletion. Hence, temperature management via restoration of shacI- ing may help to alleviate a number of water-quality problems. Water- quality problems in the streams are less likely to affect enciangerecI suckers than some of the other native fishes, however (Chapter 51. Efforts are uncler way to restore wetiancis associated with the William- son, WoocI, ancI Sprague rivers. The rationale for the projects is to restore wetiancI-river connections that promote such processes as nutrient trapping ancI sediment retention, to provide habitat for young fish, ancI to clamp variations in river flow. Wetiancis are sources of clissolvecI organic matter ancI tencI to enrich water with complex humic compounds that may be relatecI to changes in the composition of phytoplankton blooms observed in Upper I(lamath Lake (Chapter 31. THE LOST RIVER The Lost River main stem (Figure 1-3) was an important spawning site for suckers ancI supported a major fishery, but few suckers use the river now (Chapter 51. Water that historically wouicI have entered the Lost River from October to April is helcI back by Gerber ancI Clear Lake clams; sum- mer flows are reclucecI by withcirawals ancI are clominatecI by irrigation

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 147 tailwater. Free interchange of water ancI fish with the I(lamath main stem is blockecI in various ways. Not surprisingly, water quality of the Lost River is poor throughout the year, as inclicatecI by low oxygen concentrations ancI high concentrations of suspenclecI solicis (Shivery et al.2000a, USFWS 2001), ancI physical habitat is greatly changed from its original state. The Lost River is now so clegraclecI that restoration of conditions suitable for sucker spawning seems unlikely unless lancI-use or water-management practices change. THE MAIN-STEM KLAMATH: IRON GATE DAM TO ORLEANS (RM 192-60) Below Iron Gate Dam, the I(lamath River runs unobstructed to the ocean. Alterations in flow ancI high temperatures make conditions in the main-stem I(lamath less suitable than was the case historically for salmo- nicis that use the river for spawning, rearing, ancI migration (Chapter 71. Four major tributaries (the Shasta, Scott, Salmon, ancI Trinity rivers) enter the I(lamath main stem below Iron Gate Dam. These are consiclerecI in cletail below. The effect of management on the annual cycle of water flow has been the subject of consiclerable research on historical flows in the main stem. Before the creation of the I(lamath Project ancI other modifications of flow, the I(lamath River hacI a relatively smooth annual hycirograph with high flows in winter ancI spring that cleclinecI graclually cluring summer ancI recovered in fall. This pattern reflects the seasonal cycle of winter rainfall ancI spring rainfall ancI snowmelt in the basin (Risley ancI Laenen 19991. There is still an annual cycle, but its magnitude ancI seasonal dynamics have changed (Harcly ancI AcicIley 2001). Figure 4-2 illustrates hycirologic change on the basis of a comparison of mean monthly flows for the periods 1905-1912 (pre-project) ancI 1961- 1996 (post-project). Data on the earlier period are estimates basecI on measured discharges at the I(eno gaging site extrapolatecI to discharges for the Iron Gate Dam site; ciata on the later period are basecI on clirect mea- surements at the Iron Gate Dam (for methods, see USGS, Fort Collins, CO, unpublishecI material, 1995; Balance Hycirologics 1996; Harcly ancI AcicIley 20011. Flows over the period 1905-1912 have been acljustecI to correct for the above-average precipitation that occurred then. Post-project flows exhibit a shift in peak annual runoff from a mean maximum centered on April to a mean maximum centered on March (Fig- ure 4-21. The later recession in spring flows extends to mean minimum flows lower than the historical minimums. Low-flow conditions cluring summer are more prolongecI than they were before the project was built. The same analyses indicate that post-project flows cluring fall are slightly

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48 4000 3000 A_ U) u ~ 2000 o 1000 O FISHES IN THE KLAMATH RIVER BASIN Be/ \ . ~r ~ ~.~ 1961-1996 it\ . ~ ~ ..................................................................................................................................................................................................................................................... \ 190~1912 No ~~ - _~ ~........................................................................................................................................................................................................................ J I F I M I A I M I J 7 J I A I S I Month - ..................... ~ ,' ~ _ ~ /< O I N I D FIGURE 4-2 Mean monthly flows at Iron Gate Dam in 1961-1996 compared with reconstructed flows for 1905-1912. Source: Data from Hardy and Addley 2001. higher than pre-project flows. The annual volume of flow from the upper I(lamath basin is probably reclucecI. Estimated average annual runoff at the Iron Gate Dam site has cleclinecI by about 370,000 acre-ft since the con- struction of the I(lamath Project (Balance HycTrologics 1996), as might be expected in view of the amount of water that is usecT for irrigation above Iron Gate Dam (Table 1-11. The magnitude of the change in water yielcT is a matter of dispute among groups concerned with water use in the upper basin. Nevertheless, there is no cloubt that changes in seasonality of flow ancT at least some change in water yielcT have occurrecT since the full clevelop- ment of the I(lamath Project. As notecT by the U.S. Geological Survey (USGS, Fort Collins, Coloraclo, unpublishecT material 1995) in its review of the hycTrology of the I(lamath River, the changes in flow below Iron Gate Dam are attributable to water- management practices in the upper ancT lower I(lamath basin. The shift toward an earlier peak in annual runoff appears to be associated with increased flows in the I(lamath River from the Lost River cTiversions ancT the loss of seasonal hycTrologic buffering that originally was associated with overflow into Lower I(lamath Lake ancT Tule Lake. The persistent low-flow conditions that occur in summer below Iron Gate Dam reflect irrigation clemancT in the I(lamath Project ancT other parts of the upper I(lamath basin ancT irrigation cTiversions on the Scott ancT Shasta rivers ancT other tributaries Discussion below). Release of water from Iron Gate Dam has both cTirect ancT indirect effects on water temperature in the I(lamath River. The magnitude of these effects clepencTs on three principal factors: the temperature of the water as it

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 149 is releasecI from the clam, the volume of the release, anti the meteorological conditions. The temperature of water releasecI from Iron Gate Dam varies seasonally; a peak at about 22C (+/- 2C) occurs in August (Figure 4-31. In summer, the volume of flow exerts substantial control over the rate of daytime warming anti nocturnal cooling. Low flows have long transit times anti thus show greater change per unit distance. For example, a SOO-cfs release takes 2.5 clays to reach SeiacI Valley, a distance of about 60 river mi, whereas a 1,000-cfs release moves the same distance in 2 clays anti a 3,000- 27.0 - 26.5 - o `~ 25.5- 25.0- 24.5- ~ 24.0- E~ `~ 23.5- 23.0- 26.0 - B. 26.0 - 24.0 - OC) 22.0- En 20.0 - 18.0 - 16.0 - 14.0 - 12.0 - 500 cfs 1000 cfs 2000 cfs 3000 cfs ...~................................................. ..~.................................................. A - Ti, . '"'' "' . ~ ~ - , :.: ................................................................................................................................ A . ~ . ~ o On .................. . ~ ................................... ..~ .. 22.5 ~~ 22.0 1 1 1 1 1 1 190 180 170 160 150 140 130 River Mile T mean | -maximum/minimum Temperature Iron Gate Dam Outflows ................................. . ~ ~~................................................................................. ~~......................................................................................... ....................................................................... _~ . ~- 6/1/1997 8/1/1997 10/1/1997 FIGURE 4-3 Simulated and measured temperature in the I(lamath River below Iron Gate Dam. A) Simulated daily mean temperatures from Iron Gate Dam to Seiad Valley for flows of 500-3,000 cfs for conditions in August. B) Measured temperature of releases from Iron Gate Dam, Tune-October 1997. Note the minor diet change in temperature during the warmest summer releases. Source: Deas 2000. Reprinted with permission from the author; copyright 2000, University of Califor- nia Press.

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150 FISHES IN THE KLAMATH RIVER BASIN cfs release cloes so in 1.25 clays (seas 20001. Warming anti cooling per unit distance are reclucecI by short transit time anti by greater clepth. Higher flows extend the reach of river below Iron Gate Dam that supports lower mean water temperatures (Figure 4-4), but also may result in higher ciaily minimum temperatures over a portion of the reach below Iron Gate Dam (see below). Increased releases from Iron Gate Dam may benefit coho salmon (Harcly anti AcicIley 2001, NMFS 20011. The potential benefit from the releases is A- 28- 26 - 0~ _' Al 24- ~ - 5- au ~ 22- ~ ~ - 20 - 1000 cfs ...................... , . ~ "'''''''''~""""""""""""~ _ . 8 90 180 170 160 150 140 130 River Mile B. 28~ o _' au 5- 5- au au EM 3000 cfs maximum . me= 20 - .- ~ I,.,,,, ~ rninim~m ........................................ ............ 1 , ................................ ...... ,,_ 8- 190 180 170 160 150 140 River Mile FIGURE 4-4 Simulated daily maximum, mean, and minimum water temperatures on the Klamath River from Iron Gate Dam to Seiad Valley for Iron Gate Dam releases of 1,000 cfs (A) and 3,000 cfs (B) under meteorological conditions of August 14, 1996. Source: Deas 2000. Reprinted with permission from the author; copyright 2000, University of California Press.

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 151 confounclecI, however, by relationships between minimum, mean, ancI maxi- mum temperatures. For example, water releasecI from Iron Gate Dam in August has a mean temperature near 22C, which is well above the acute tolerance threshoicI for coho (Chapters 7 ancI 81. FielcI-calibratecI moclels clevelopecI by Deas (2000) and models presented by Hardy and Addley (2001) show a considerable increase in the daily mean water temperature with distance downstream for flows that are typical of August. As noted in Chapters 7 ancI 8, however, bioenergetics of salmonicis clepencI not only on the mean temperature but also on the clie! range of temperature; low mini- mum temperatures are especially important for coho salmon. Simulations concluctecI by Deas (2000) provide insight into the thermal response of the I(lamath River to increases in flow cluring late summer (Fig- ure 4-41. Uncler moderate flow conditions in micI-August (1,000 cfs), with typical accretions from tributaries, maximum ciaily temperatures increase rapicIly downstream of Iron Gate Dam to a peak of 26C within 15 mi. Daily minimum temperatures caused by nocturnal cooling reach a minimum of 20C within about the same distance. By the time this water reaches SeiacI Valley (RM 130), maximums are greater than 26C, ancI minimums are 22C; the average gain from Iron Gate Dam is 2C. Tripling the flow from Iron Gate Dam (Figure 4-4B) provides moclest reduction in mean ancI maxi- mum ciaily temperatures, particularly in the first 20 mi of the river clown- stream from the clam. The increased volume of water ancI shorter transit time, however, recluce the effect of nocturnal cooling in the reach between Iron Gate Dam ancI SeiacI, ancI raise minimum temperatures for about two-thircis of the reach. Although increased flows recluce mean ancI maximum tempera- tures, the increase in minimum temperatures may aciversely affect fish that are at their limits of thermal tolerance (Chapters 7 ancI 81. Two aciclitional complications arise from increased releases from Iron Gate Dam. First, cluring low-flow conditions, tributaries can influence main- stem temperatures. Temperatures in the I(lamath River at 1,000 cfs are affected substantially by the Scott River ancI minimally by the Shasta River. Modification of flow ancI temperature regimes in these tributaries through better water management couicI improve main-stem temperatures. Increase in flow to 3,000 cfs, however, eliminates any thermal benefit from the trib- utaries (seas 20001. In regulatecI rivers such as the I(lamath, there often is a nocle of mini- mum clie! temperature variation about 1 clay's travel time from a clam (Lowney 2000) and an antipode of maximum variation at half this dis- tance. The muted minimums ancI maximums of the thermal nocle reflect a single clie! cycle of roughly equal heating ancI cooling cluring 1 clay's travel time. Conversely, the large variation in temperatures at the antinocle re- flects only half a diet heating or cooling cycle. Reduction in maximum temperature is one of the benefits of the thermal nodes. These nodes, how-

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152 FISHES IN THE KLAMATH RIVER BASIN ever, also exhibit greatly increased minimum temperatures. In the I(lamath River uncler flow ancI meteorological conditions typical of August, the highest minimum ciaily temperatures will occur at the nocle ancI may be points of greatest thermal stress for salmonicis. Increases in flow will cause the nocle to shift downstream because of clecreasecI transit times (Figure 4-4), thus increasing the amount of river that is subjected to increased . . temperature minimums. The main-stem I(lamath like the lakes, reservoirs, ancI rivers of the upper basin has concentrations of nitrogen ancI phosphorus that are quite high relative to many aquatic systems (Campbell 2001; Figure 4-51; they indicate eutrophic conditions. In aciclition, much of the nitrogen ancI phos- phorus is reaclily available for plant uptake (for example, the forms nitrate ancI soluble reactive phosphorus). As a consequence of high nutrient con- centrations, the river has the potential to support high rates of primary production. Even when nutrient concentrations are high, however, blooms of phytoplankton, such as those in Upper I(lamath Lake, clo not occur in streams or rivers of moderate to high velocity because flow limits the accu- mulation of suspenclecI algae. Conditions may be favorable in the main stem for the growth of phytoplankton cluring low flow, when the water is mov- ing slowly, ancI growth of attached algae ancI aquatic vascular plants also can be stimulatecI by nutrients. Stimulation of any kincI of plant growth can affect oxygen concentrations. During summer, oxygen concentrations in the I(lamath River often fall below 7 mg/L anti, for brief periods, below 5.5 mg/L (Campbell 20011. For 000 - 400 - 200 - o- TN Nitrate Iron Gate Seiad Valley SRP Nutrient FIGURE 4-5 Mean annual concentrations of total nitrogen (TN) and total phos- phorus (TPl, nitrate (NO3- expressed as N), and soluble reactive phosphorus (SRP) at two stations on the I(lamath River. Source: Data from Campbell 2001.

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 153 example, average concentrations were below 7 mg/L on 36 clays at the SeiacI Valley monitoring station in 1998. More severe anti extenclecI periods of low oxygen concentrations occur at Iron Gate Dam because of clegracI- able organic matter (such as cleacI phytoplankton) originating in reservoirs. Low oxygen concentrations, especially below 5.5 mg/L, are unfavorable to salmonicis (Chapter 71. THE SHASTA RIVER (RM 177) Flow of the Shasta River is clominatecI by discharge from numerous cool-water springs anti not by surface runoff. The stable, coo! flows anti high tert~ty ot the Shasta h~stor~cai~y created a highly productive, ther- mally optimal habitat for salmonicis. The Shasta River maintains about 35 mi of fall-run Chinook habitat. 38 mi of coho habitat, anti 55 mi of steelheacI habitat (West et al. 19901. The amount of habitat has not cleclinecI since 1955 but is substantially smaller than the original amount. Use of remaining habitat is contingent on flow anti water quality, both of which may be inadequate in ciry years. Mean annual runoff from the Shasta River is 136,000 acre-ft, which is less than 1% of the runoff of the I(lamath River at Orieans. Runoff within the basin peaks cluring winter, when ciaily flow is near 200 cfs (Figure 4-61. 1 1 ~ 1 ~ 1 ~1 1 11 1 1 1 1 800 - . 700 - Irrigation Season .~.~..~...~...~:................................................................ Winter Baseflow 100 - .~ . O 1 1 1 1 1 l l l l l Nov Feb ....~..~ ~ l l l l l l l l l l l l Nov Feb May Aug 1999 May Aug 2000 2001 FIGURE 4-6 Annual hydrograph for the lower Shasta River (at Yreka, Californial, from May 1999 to May 2001. Note base-flow recovery during fall and sustained base flow throughout the winter of 2001.

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154 FISHES IN THE KLAMATH RIVER BASIN Peaks are associated with rain at times when there are no irrigation cliver- sions (note that peaks clicI not occur in 2001, a year of cirought). Flow cleclines rapicIly with the onset of irrigation in late March. Flow minimums typically averaging less than 30 cfs occur cluring summer. Flow increases rapicIly in the fall when irrigation encis. Winter base-flow conditions typi- cally are 180-200 cfs, regarcIless of precipitation. The hycirology of the Shasta River is affected by surface-water cliver- sions, alluvial pumping, ancI the Dwinnell Dam (Figure 4-71. Historically, springs ancI seeps clominatecI the hycirograph of the Shasta River. Mack (1960) reported that one small tributary, Big Springs (Figure 4-7), supplied a consistent 103 cfs to the Shasta River before water clevelopment. Flow from the springs ancI numerous small accretions in the reach above them wouicI have suppliecI flows close to or exceeding tociay's bankfull condition, even cluring summer months. Flows of that magnitude wouicI have hacI very short transit times (less than 1 clay to the I(lamath River), thus maintaining coo! water throughout summer for the entire river. Consistency of flow ancI coo! summer water were the principal reasons that the Shasta River was historically highly productive of salmonicis. During summer, the Shasta River may also have coolecI the main-stem I(lamath near the confluence of the Shasta ancI the main stem. Since 1932, surface-water resources in the Shasta valley have been uncler statutory acljuclication (Decree 70351. Three of the four major irriga- tion districts have a cumulative appropriative right to divert more than 110 cfs from the Shasta River from April 1 to October 1 (Gwynne 19931. Dwinnell Dam is used by the fourth major irrigation district to store winter flows of the Shasta River ancI Parks Creek. Dwinnell Dam, constructed in 1928, has a capacity of 50,000 acre-ft. The California Department of Wa- ter Resources Watermaster Service has been apportioning water within the basin since 1934. Riparian water rights below Dwinnell Dam are not aclju- clicatecI ancI are not regulatecI by the watermaster, ancI the 1932 acljuclica- tion clicI not aciciress grounc~water, which is critical for support of base flow. Seven major diversion clams ancI numerous smaller clams or weirs are on the Shasta River ancI its tributaries below Dwinnell Dam (Figure 4-71. When the diversions are in operation, they substantially ancI rapicIly recluce flows in the main stem (Figure 4-61. During the drought of 1992, flows in the Shasta ciroppecI from 105 cfs on March 31 to 21 cfs by April 5. The numerous diversions on the Little Shasta River now routinely leacI to com- plete clewatering of its channel in late summer. Although surface diversions play an important role in causing the low flows of the Shasta, there is little quantitative information on the relative role of each diversion, ancI records either have not been kept or are not available from the watermaster service that apportions flows.

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168 FISHES IN THE KLAMATH RIVER BASIN forts have monitoring programs that allow assessment of their effective- ness, ancI there appears to be no inclepenclent review of the restoration ancI monitoring programs. More importantly, these efforts have yet to aciciress comprehensively water bucigets ancI water uses, inclucling the contribution of grounc~water to surface flows ancI water quality. Until a comprehensive water buciget is clevelopecI, significant progress at restoring coho ancI other salmonicis is unlikely to occur. THE SALMON RIVER (RM 62) Within the lower I(lamath watershed, the Salmon River remains the most pristine tributary; it has a natural, unregulatecI hycirograph, no signifi- cant diversions, ancI limitecI agricultural activity. Although it is not well clocumentecI, runs of all the remaining anaciromous fishes in the I(lamath watershed (Chapter 7, Table 7-1) occur in the Salmon River (Moyle et al. 1995, Moyle 20021. The Salmon River's unique characteristics stem from its mountainous terrain ancI public ownership of lancI. At 750 mi2, the Salmon River is the smallest of the four major tributary watersheds in the I(lamath basin. Even so, the annual runoff from the Salmon is twice that of the Scott ancI 10 times as great as that of the Shasta River. High runoff reflects the steep slopes anti high annual precipitation (50 in) of the watershed. Runoff in the basin is clominatecI by a winter pulse associated with high rainfall anti a spring snowmelt pulse from April through lune (Figure 4-141. During sum- mer ancI late fall, low-flow conditions predominate, particularly in smaller tributaries. Unlike the Scott ancI Shasta, the Salmon River watershed is almost entirely feclerally owned (Chapter 21. The Salmon River watershed supports about 140 mi of fall-run Chi- nook spawning ancI rearing habitat ancI 100 mi of coho ancI steelheacI habitat (CDFG 1979a). Logging roacis, roacI crossings, ancI frequent fires in the basin appear to contribute to high sediment yielcis. Historical ancI con- tinuing placer mining has reclucecI riparian cover ancI clisturbecI spawning ancI hoicling sites in the basin as well. Increased water temperatures have been noted in the Salmon River cluring late-summer low-flow periods, but their cause is unclear; they may be natural or may be in part a byproduct of logging ancI fires. The high summer temperatures may also be in part a function of the orientation of the watershed ancI naturally low base flow cluring late summer (I(ier Associates 19981. THE TRINITY RIVER (RM 43) The Trinity River has the largest tributary watershed in the lower I(lamath basin (2,900 mid. The watershed extends up to 9,000 ft in the

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 169 8000 - .~O - ~_ co _' ~ 4nnn- o 3000 - 2000 - 1000 - Spring Snowmelt Pulse . ~ _ ~ ~ .......... _ Winter Flood Pulse .................................................................... : ~ .: ~ I ..~ 1 O1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 May Aug Nov I Feb May Aug Nov I Feb 1999 2000 2001 FIGURE 4-14 Annual hydrograph of the Salmon River at Somes Bar, California, May 1999-May 2001. Trinity Alps ancI the Coast Ranges ancI flows more than 127 mi to its confluence with the I(lamath at 230 ft asl, 43 mi above the I(lamath River mouth (Figure 4-151. It is the largest contributor of tributary flow to the main-stem I(lamath. Prior to construction of the Trinity River Diversion (TRD), the Trinity River accounted for close to one-thircI of the average total runoff from the I(lamath watershed Based on USGS gaging recorcis)- more than twice the runoff from the entire upper basin. Hycirologically, the Trinity watershed is broacIly similar to the Scott ancI Salmon watersheds. Prior to construction of the Trinity River Diversion (TRD) project in 1963 (cliscussecI below), runoff averaged close to 4.5 MAF annually. The bulk of this runoff was concentrated into two seasonal pulses (Figure 4-16) winter floocis associated with mixed rain-snow events that typically occur between micI-December ancI micI-March, ancI a spring snow- melt pulse that begins in late March-early April anti, clepencling upon snow- pack conditions, ceases in luly. The summer ancI fall are clominatecI by baseflow conditions. Historically, late summer ancI early fall flows on the Trinity were quite low, indicating limitecI natural baseflow support. During years of below-average moisture, tributaries to the Trinity commonly ciry up. Precipitation patterns ancI associated runoff vary consiclerably through- out the Trinity watershed. Precipitation averages 57 in. annually, but ap- proaches nearly 85 in. in the Hoopa Mountains ancI the Trinity Alps. In the

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770 a (~ ma\\ I ~) 6 InJl~, Sew H~ ~~( In~lan \ 7~\~ /~f~I~l~\ ~ 1 A) jaw 1( JOI1~S 23 a 2230' S -~1~/ ~110~ ~ ~ )~ ~~,~/~ Ssssss~ss/ss-sssssssssisssssssss~ssssssssssss-sssssssssssssssssss _ fir Bureau it. ~ ~~\ ~ ~S ~ 1 ~ ~~E ~ ~ ~~\ ~lOlt~ ~ ~ _ _ ~ O - \ ~11111~11111111\ tacrame) ~,,,,,,,~\San [~anclsco ~I~\` s . 4~30 - . Am, ~ 4~) ~1~.~ YI ~~ ~ / ~ ~ r I . t~ ::!I~ ~24.# ~.~- ~I ~: \~ ~~I~\~rn1;j~. 7 ~ a/< ?--~- ~.~ ~~j~# - cyan'' ~ ~~. {\ , , ( 1 4030 Anderson I~I < o lo .~ 20 ~~s 1 1 1 1 1 1 0 70 20 ~~ec~ FICURF 4-13 index map of the Trinity River ~atcrshcd. Source: Bodied Tom USP(S/HVT 1999. high-~hitude, northeastern portions of the watersheds the annual hydro- graph ~ dominated by sno~mNt runoff during the spring and early sum- mer. In contrast the lo~er-elevation watersheds, such as the South Fork and North Fork, are dominated by minter rainfaN Hood pulses. As noted in Chapter 2, the tectonic, geologic, and chmatic sethng of the Trinity River has ampliRed the influence of land-use activities on fish. Highly unstable rock types, which are associated Huh the Coast Range Geologic Province on the Rest and the Klamath Mountains Ceologic Prov- ince on the easy coupled Huh high rates of uplift, lead to naturaNy high erosion rates (Hount 199iJ. Like the western portions of the Scott ~ater- shed, the eastern portions of the Trinity watershed contain deeply ~eath-

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 171 20,000 18,000 _ _` U] 'a 16,000 t4 14 000 ~ ' 'A 12,000 4, 10,000 _ 8,000 6,000 4,000 2,000 o Trinity Reservoir Inflow Lewiston Gage (regulated) --- TREE recommendation Winter flood pulse Spring snowmelt pulse ~ Fall bud ~ I Summer baseflows _~_ ~_~ Oct | Nov | Dec | Jan | Feb | Mar | Apr | May | Jan | Jul | Aug | Sep | Water Year 1973 FIGURE 4-16 Example of regulated (dotted line, current recommended outflow) and unimpaired (solid line, inflow to Trinity Diversion Project) flows on the Upper Trinity River for water year 1973, a normal water year (40-60% exceedance prob- ability for annual flow volume). Source: Modified from USFWS/HVT 1999. ered granitic rocks that yield highly erodible soils dominated by decom- posed granite. In both the eastern and western portions of the watershed, highly unstable metamorphic rock units are associated with numerous and widespread slope failures. Landslides play a dominant role in hilisiope evolution on the South Fork Trinity and in canyon reaches of the main stem. Approximately 80% of the Trinity watershed is federally owned and is managed by USER and USES. The remainder is a mix of private ownership and lands within the Hoopa Valley and Yurok Indian reservations. Land- use practices on public and private land within the Trinity watershed have played a central role in the precipitous decline of salmon runs in the latter half of the 20th century. As with most tributary watersheds of the I(lamath system, logging, mining, and grazing have reduced the quantity and quality of salmon habi- tat in the Trinity watershed. The greatest effects have occurred in the South Fork of the Trinity and on the main stem below Lewiston Dam and above the confluence of the main stem with the North Fork. The South Fork is the largest tributary of the Trinity River, and was historically a significant producer of Chinook and coho salmon and steel- head trout (Pacific Watershed Associates 19941. The South Fork and its . ~ . . . .

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72 FISHES IN THE KLAMATH RIVER BASIN main tributary, Hayfork Creek, comprise 31% of the Trinity watershed anti 6% of the total I(lamath watershed. The South Fork, which is un- ciammecI, is the largest unregulatecI watershed in California. Currently, more than 56 mi of the river are protected uncler the California WilcI anti Scenic Rivers Act. The South Fork has high background sedimentation rates, but intense logging in the 1960s on highly unstable soils, couplecI with a large storm in 1964' proclucecI sedimentation rates significantly above background levels. Adverse effects of sediment on aquatic life caused EPA to require a total maximum ciaily loacI (TMDL) stucly for sediment in the South Fork (EPA 1998). Loss of riparian cover anti creep pools also appears to have affected water temperature. Most regional ancI national attention has been focused on the main stem of the Trinity River. Mining, logging, ancI grazing practices within this portion of the watershed contributed high volumes of sediment to the main stem ancI clegraclecI habitat prior to creation of the TRD (EPA 2001). Log- ging on sensitive soils proclucecI high loacis of fine sediment in the main- stem Trinity. Prior to TRD operations, however, seasonal high flows asso- ciatecI with the winter ancI spring floocI pulses appear to have maintained habitat of reasonable quality, thus preventing a significant clecline in steel- heacI ancI salmon (McBain ancI Trush 1997). In 1955 Congress authorized construction of the TRD project to divert water from the upper Trinity River into the Sacramento River as part of the Central Valley Project (CVP). The primary beneficiaries of these diversions are farms of the San loaquin Valley serviced by the Westiancis Water Dis- trict. The TRD consists of two clams: the Trinity Dam, which has an im- pounciment capacity of 2.4 MAF, ancI Lewiston Dam, which impounds Lewiston Reservoir ancI provides the diversion for the CVP. The closure of Lewiston Dam in 1963 lecI to loss of access to spawning sites ancI clegraciation of habitat. Located at Trinity RM 112' Lewiston Dam currently blocks access to more than 109 mi of potential spawning habitat in the upper watershed (USFWS 1994). Aciclitionally, the Trinity ancI Lewiston Dams trap all coarse sediment that wouicI normally be sup- pliecI by the upper watershed. When completecI, the TRD clivertecI more than 88% of the annual runoff from the upper watershed to the CVP. After 1979' these diversions were clecreasecI to 70% of the annual runoff. The magnitude of the cliver- sions ancI associated flow release scheclules eliminatecI winter ancI spring floocI pulses in the main stem of the Trinity (Figure 4-16). The effects of these manipulations are most acute between Lewiston Dam ancI the North Fork Trinity (RM 112-72). Below the North Fork, tributary flow ancI sediment supply recluce the adverse effects of upstream water management (USFWS/HVT 1 999).

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 173 Changes in hycirology on the Trinity River, loss of sources of coarse sediment, ancI continued influx of fine sediment from hilisiope erosion have created significant changes in habitat conditions downstream of the TRD. Channel response to changes in flow regime incluclecI reductions in cross section, reduction in lateral migration, establishment of riparian vegetation on channel berms, loss of backwater habitat, ancI loss of spawning gravel. The new channels have been static, reclucecI in size, ancI deficient in suitable habitat. In 1981 the Secretary of the Interior authorized a Trinity River Flow Evaluation (TRFE) stucly of ways to restore the fishery resources of the Trinity River (USFWS/HVT 19991. The final TRFE report recommencis releases from TRD based on five water-yr types: extremely wet, wet, normal, ciry, ancI critically ciry. The hycirographs consistent with these recommendations still allow for clelivery of water to the CVP, but shape the hycirographs so that they support the life-history neecis of salmonicis, inclucling reintroducing disturbance to control establishment ancI growth of riparian vegetation, coarse sediment transport to establish pools anti riffles ancI to clean spawning gravels, ancI sufficient flows to recluce water temperatures for rearing. The TRFE also contained an adaptive manage- ment approach that calls for assessment of the effect of changes in flow regime ancI adjustments as necessary to improve the success of the program. The TRFE anti the associated fecleral environmental impact statement (EIS) anti environmental impact report (EIR) were the product of multiple years of collaborative effort on the part of agencies anti stakehoicler groups. This program was subjected to rigorous external peer review, which lecI to numerous, substantive revisions in proposed remecliation measures. The TRFE was used in the Department of the Interior's Record of Decision (ROD; Trinity River Mainstem Fishery Restoration, USFWS 20001. A law- suit filecI by the Westiancis Water District in 2001 contenclecI, however, that the unclerlying studies clicI not aclequately aciciress the economic impacts of the CVP water on users anti electricity consumers, anti failecI to account for the effects of changes in flow on ecosystems of the Sacramento-San loaquin Delta. In 2001, U.S. District Court lucige Oliver Wanger rulecI against the Department of the Interior (DOI) anti orclerecI it to complete a supplemen- tal EIS, which is still in preparation. Consequently, the recommenclecI TRFE flow releases have not occurred. In response to the lower I(lamath fish kill of September 2002, the presiding jucige was asked by the Hoopa Valley Tribe to allow some operational flexibility in orcler to help avoid fish kills in September 2003. The jucige allowecI 50,000 acre-ft to be set asicle for emergency increases in flow to recluce the chances of a fish kill. In August 2003, the Trinity Management Council requested that DOI allow a sus- tainecI flow release in September 2003 clue to low-flow conditions anti

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74 FISHES IN THE KLAMATH RIVER BASIN predictions of a large salmon run. As of September 2003' these moclifica- tions in flow were uncler way. Given the size of the Trinity River watershed ancI its large amount of runoff, the operations of the TRD must affect the quality of habitat in the lowermost I(lamath River ancI its estuary. There is little publishecI informa- tion, however, on the effects of the Trinity on the lowermost I(lamath ancI the estuary. Information proviclecI here is principally clerivecI from an analy- sis of USGS gaging ciata (1951-2002) from the Trinity ancI the I(lamath, ancI from the Trinity River Flow Evaluation stucly (USFWS/HVT 19991. Following construction of the TRD, the contribution of the Trinity to the total flow of the I(lamath River cleclinecI from 32% to approximately 26% (Figure 4-171. This clecline is not equally clistributecI throughout the year. The largest effect of the TRD occurs in the spring, cluring filling of the Trinity Reservoir. Prior to construction of the TRD, snowmelt runoff from the Trinity proviclecI approximately 290~000 acre-ft, or approximately one- thircI of the inflow to the estuary, to the I(lamath River in rune. Following construction of the TRD, the average contribution of the Trinity in lune cleclinecI to 160~000 acre-ft; cluring this same period, inflow to the I(lamath estuary cleclinecI by approximately 200~000 acre-ft per yr. During the late summer ancI early fall the Trinity, prior to construction of the TRD, contributed a relatively small amount to the total flow of the I(lamath River (less than 15% in September). In the period following con- 3000000 - - 2500000- 2000000- .m ~ 1500000- g 1 000000 - 500000- O- _ Klamath 1964-2002 Trinity 1964-2002 Klamath 1951-1963 )( Trinity 1951-1963 ..~........ Jan | Feb | Mar |APr1I | May | June | July | Aug | Sept | Oct | Nov | Dec FIGURE 4-17 Average monthly discharge of the I(lamath River at I(lamath (USGS 11530500) and the Trinity River at Hoopa (USGS 11530000) for the period 1951- 2002. The Trinity River Diversion project was constructed in 1963. Note the re- duction in spring flows associated with operation of the TRD.

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 175 struction of the TRD, there was a clecline of 11% in average September flow of the Klamath main stem above the Trinity. Because of minimum flow requirements for the TRD, however, average flows from the Trinity increased cluring this period, partially offsetting the cleclines in flow from Iron Gate Dam ancI boosting the Trinity's relative contribution to 20%. Spring ancI early summer water temperatures are of concern in the lower Klamath ancI Trinity clue to their effect on outmigrating steelheacI ancI salmon smolts. FielcI ancI mocleling studies concluctecI in 1992-1994 at the confluence of the Klamath ancI Trinity demonstrate the relative impor- tance of flow to water temperatures (Appenclix L in USFWS/HVT 1999). Although temperature differences between the Klamath ancI the Trinity River can be consiclerable (up to 5C or more), temperature regimes usually are quite similar at the confluence because of the long distances of travel (> 100 mi) for water releasecI from both Iron Gate Dam ancI Lewiston Dam, ancI the broacIly similar release scheclules of the two reservoirs. Differences between the two rivers become pronounced only when there are large disparities in flow volumes. For example, when the Trinity flow releases are very large (by a factor of 2 to 3) compared to flow within the Klamath main stem, the Trinity cools the Klamath because its waters reach the confluence more quickly than at low flow. The Trinity River Mainstem Fishery Restoration program (USFWS 2000)is' by necessity, focused principally on restoring spawning ancI rear- ing habitat within the main-stem Trinity River. Thus, from the viewpoint of coho recovery, the EIS process cannot be expected to result in the improve- ments of tributary habitat that coho require. Also, the program cloes not appear to have invested significant effort in evaluating its beneficial effects on the lower Klamath ancI its estuary. With the exception of the participa- tion of the Hoopa Valley ancI Yurok Tribes, there also appears to be only minimal effort to coordinate management of the Trinity watershed with efforts to manage the rest of the Klamath watershed. The proposed flow release scheclule contained within the 2001 ROD, which is currently helcI up in litigation, may, however, provide substantial benefit downstream of the Trinity, thereby increasing the welfare of salmon ancI steelheacI through- out the Klamath watershed. MINOR TRIBUTARIES TO THE LOWER KLAMATH MAIN STEM (RM 192-0) Many small tributaries enter the main-stem Klamath between Iron Gate Dam ancI the mouth of the river. They cirain mountainous, largely forested watersheds, but most are creeks affected to some clegree by logging, past mining, grazing, ancI agriculture. In many of the tributaries along the stream corridors, water withcirawal leacis to reductions in summer base flows.

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176 FISHES IN THE KLAMATH RIVER BASIN Water quality has not been extensively stucliecI, but the tributaries may be particularly important in providing coicI-water habitats for salmonicis (Chapter 71. Of these creeks, 47 are known to have coho populations (NMFS 20021' but little is known about the specific conditions of these populations in relation to habitat ancI changing conditions in the basin. In the more mountainous sections of the basin, slopes are steep, soils are unstable, ancI streams are affected by erosion that is exacerbated by roacis ancI disturbance in the riparian zone. Large floocis that have occurred about once per clecacle also have lecI to erosion, clebris jams, ancI aggracia- tion of sediments where tributaries enter the I(lamath. In some cases, the bars, which consist of aggraclecI sediments, block flow cluring low-flow conditions, thus preventing fish passage, but many of the blockages have been removed in recent years (Anglin 19941. MAIN-STEM KLAMATH TO THE PACIFIC (RM 60-0) Over its final 60 mi the I(lamath flows first southwest from Orieans to Weitchipee, where the fourth major tributary, the Trinity River, enters at RM 43. The I(lamath then flows northwest to the ocean. The estuarine portion of the I(lamath River is relatively short in relation to the watershed. Because intrusion of salt water varies seasonally, the length of the estuary is variable. The greatest intrusions occur at low flow, but brackish water (15- 30 ppt) extends only a few mi upriver even at low flow (Wallace ancI Collins 19971. Ticial amplitucles in the estuary vary up to 2 m. Flows in the lowermost I(lamath are driven by a seasonally varying mixture of main-stem flow ancI accretions of water from tributaries. For example, water reaching the river via the Iron Gate Dam contributes less than 20% of the flow at Orieans in May ancI lune (1962-19911. The other 80% of the flow is clerivecI primarily from tributaries. The percentage of flow that comes from Iron Gate Dam increases over the summer. In Septem- ber, over 60% of the flow originates from Iron Gate Dam Hydrosphere Data Products, Inc. 19931. As noted above, the Trinity River ancI opera- tions of the TRD exert substantial influence over hycirologic conditions of the lower I(lamath ancI its estuary. Changes in release, even uncler the new ROD, have lecI to cleclines in late winter through early summer flows at the mouth of the I(lamath. Fall flows, on the other hancI, are augmented by increased flows from the Trinity. Although alteration of hycirographs in a number of heac~waters ancI tributaries has been quite substantial (e.g., Lost River, Shasta River), the overall effect of water clevelopment on total annual flow of the downstream reaches of the I(lamath River is surprisingly small. Runoff from the upper I(lamath basin has been reclucecI from approximately 1.8 million acre-ft to 1.5 million acre-ft in a year of average moisture (USGS 1995, Harcly ancI

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CURRENT AND HISTORICAL STATUS OF RIVER AND STREAM ECOSYSTEMS 177 AcicIley 2001, Balance Hycirologics 1996), ancI irrigation has clepletecI the mean annual flow at Orieans (above the Trinity), where the flow is ap- proximately 6 million acre-ft, by less than 10 %. There has been a notice- able shift in the timing of runoff, however. Peak annual runoff occurs in March instead of April ancI the flows of late spring ancI early summer tencI to be lower than they were historically. In late summer, water temperatures at Orieans exceed 15C typically from lune into September (Figure 4-181. River temperatures in excess of 20C occur on most ciates in luly ancI August ancI in many years, high temperatures extend into fall. For example, temperatures over 18C have been observed in late October. Temperatures in the I(lamath may have always been high (over 15C) in summer ancI fall, but it is likely that the loss of coicI water from tributaries has resultecI in a net increase in temperatures over the annual cycle, particularly cluring sum- mer uncler either normal or low-flow conditions. Even though hycirologic change in the lowermost I(lamath main stem seems too small to have causecI large changes in the estuary, significant impairment of the estuary couicI have occurred through warming of the river water ancI through increased organic loacling causecI by eutrophica- tion ancI alteration of flow regimes in heac~waters. The estuary couicI show adverse chemical conditions as a result of these changes, ancI coho in the estuary thus couicI be affected. The extent of these changes ancI their poten- tial effect on coho have not been well clocumentecI, however. Information on water quality of the lowermost I(lamath River is sparse. 30 - 25- _' a) a) a) Em a) 20 - 15 - 10 - 5- , O- . i. ~ +~. ~ .> .. ~ ~ 41~. ~ J F A M J J A S O N D M onth FIGURE 4-18 Water temperature (instantaneous daytime values) of the I(lamath River at Orleans based on observations at USGS station 18010209,1957-1980, plotted on a single annual time span.

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178 FISHES IN THE KLAMATH RIVER BASIN CONCLUSIONS Most flowing waters of the I(lamath basin show substantial environ- mental degradation involving loss of coarse gravels, excessive suspended sediment, impaired channel morphology, loss of woody riparian vegeta- tion, major alteration of natural hydrographic features, and excessive warmth. These changes affect not only the main stems of the I(lamath River and major tributaries, but also small tributaries where salmon are or could be present. While to some extent historical, degradation continues through a variety of water-management and land-use practices including irrigation, grazing, mining, and timber management. Documentation is poor for some locations, and especially so for small tributaries. In the upper basin, the tributaries that drain into Upper I(lamath Lake are poorly understood except in regard to nutrient transport. I(nowledge of basic hydrology and water use is sparse, as are conditions relevant to spawn- ing of listed suckers and refugia for sucker fry. Topics of special interest include substrate and channel quality, sediment load, and status of riparian vegetation. In the lower basin, research has documented extensive modifi- cations of riparian habitats, especially along the Scott and Shasta rivers. Adverse changes in stream-channel structure, sediment transport, flow, and temperature are commonplace even on federal lands. Nutrients, dissolved oxygen, temperature, flows, and physical habitat of the main stem of the I(lamath River have been extensively studied. Still, additional research that would clarify the interactions between hydrology and temperature, especially as affected by water-management strategies, is needed. Considerable research on this topic is in progress, but field investi- gations have focused primarily on the river between Iron Gate Dam and Orieans. Conditions in the lowermost reaches of the I(lamath River, includ- ing the estuary, have received less attention but are important to salmonids, as shown by the mass mortality of salmonids in 2002 (Chapter 71. The I(lamath system as a whole is nutrient-rich and productive. High concentrations of phosphorus, a key nutrient, are typical of I(lamath waters because of natural sources. Anthropogenic sources may be important in some cases as well. Water-quality conditions, except temperature, are within satisfactory bounds in most cases for flowing waters. The greatest impair- ments involve physical features, including temperature for salmonids.