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3 Current Status of Aquatic Ecosystems: Lakes INTRODUCTION Natural lakes that were suitable for occupation by suckers before lancT- use clevelopment ancT water management incluclecT Upper I(lamath Lake, Lower I(lamath Lake, Tule Lake, ancT Clear Lake (Figure 1-31. All of these lakes have been changed morphometrically ancT hycTrologically ancT are now usecT in the I(lamath Project water-management system for storing ancT routing water. Gerber Reservoir is also part of the water-management sys- tem, but its location was previously occupied by a marsh rather than by a lake. Other lakes relevant to the welfare of suckers inclucle those lying behind five main-stem clams that, except for I(eno Dam, incorporate hycTro- electric production facilities (Figure 1-3, Table 3-11. The last in the se- quence of main-stem clams, Iron Gate Dam, provides reregulation capabil- ity for the main stem of the I(lamath River as explainecT below. Of the lakes usecT for storage ancT routing, Upper I(lamath Lake, Clear Lake, ancT Gerber Reservoir support the largest populations of listecT suck- ers (see Chapter 6 for a cletailecT treatment of the suckers), ancT these three lakes have been the main focus of ecological ancT limnological analysis relatecT to the welfare of suckers. Upper I(lamath Lake has been stucTiecT especially intensively because it potentially wouicT support the largest popu- lation of suckers ancT shows the greatest number of environmental prob- lems, as incTicatecT by episodic mass mortality of aclults ancT probable harcT- ships in all life-history stages. Clear Lake ancT Gerber Reservoir afford a useful comparison with Upper I(lamath Lake because the sucker popula- tions there have not suffered mass mortality ancT are generally more stable 95

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES 97 than the populations of Upper Klamath Lake. The hyciroelectric reservoirs on the main stem have been stucliecI sparingly anti are of less interest than other lakes from the viewpoint of listecI suckers. The lakes shown in Table 3-1 clo not serve as habitat for coho salmon, which are blockecI by Iron Gate Dam from entry into the upper Klamath basin. Limnological characteristics of the waters behind Iron Gate Dam are potentially important to the coho salmon, however, in that waters releasecI from the clam have a large influence on the water-quality characteristics of the Klamath River main stem, especially near the clam. Reflecting the rela- tive amounts of research or monitoring ancI the apparent ranking of lakes with respect to their importance for the enciangerecI ancI threatened fishes, this chapter clevotes most of its attention to Upper Klamath Lake, some to the other lakes that are used for storage anti routing of water, ancI some to waters above Iron Gate Dam that hoicI non-reproclucing populations of listecI suckers anti have the potential to affect coho downstream; the rem- nants of Tule Lake anti Lower Klamath Lake provide little lacustrine habi- tat at present, but offer potential for restoration. UPPER KLAMATH LAKE Description Upper Klamath Lake is the largest body of water in the Klamath basin anti is one of the largest lakes in the western United States (about 140 mid. The lake anti its drainage lie on volcanic deposits clerivecI in part from the nearby Crater Lake calclera, which took its present form as a result of the eruption of Mount Mazama (about 6,800 BP). The lake also shows a strong tectonic influence, however, as is evident from a pronounced scarp along its southwestern ecige (Figure 3-11. Although Upper Klamath Lake has a very low relative clepth (ratio of clepth to mean cliameter), it has substantial pockets of water over 20 ft creep (maximum, 31 ft at a water level of 4,141.3 ft above sea level; USER 1999 as cited in Welch anti Burke 20011. The northern, southern, anti eastern portions of the lake anti Agency Lake, which is connected to Upper Klamath Lake anti is here treated as part of it, are uniformly shallow; they offer water little creeper than 6 or 7 ft at mean summer lake elevation (4,141.3 ft above sea level). Even though specific runoff for the watershed of Upper Klamath Lake is relatively low (about 300 mm/yr), the hyciraulic residence time of Upper Klamath Lake is only about 6 ma because the lake is shallow (there is consiclerable interannual variability). The flat bathymetry of the lake also causes its surface area to be quite sensitive to changes in water level. Before the construction of Link River Dam, which was completecI in 1921, the water level of Upper Klamath Lake fluctuatecI within a relatively

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98 FISHES IN THE KLAMATH RIVER BASIN Pelican\, ~ ~-~: Agency \,:~,1 ~G~\ Lake ~~ ~ " U~ | OREGON Area of Detail :3 Marsh 12+ Feet 6 Feet ~ _ _ 1 0 1 2 3 4 5 miles en\ Upper ~ Klamath N: Lake `~\ / . / ~ i:. \ \ \~ A Link River Dam \ FIGURE 3-1 Bathymetric map of Upper Klamath Lake and Agency Lake showing depths at the mean summer lake elevation of 4,141 ft above sea level. Contours are from data of U.S. Bureau of Reclamation (1999) as reported by Welch and Burke (2001~. Source: Welch and Burke 2001.

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES 99 narrow range (about 3 ft), as wouicI be expected for a natural hycirologic regime (Figure 3-21. Although irrigation was uncler way in the basin at that time, there was no means of using the lake for storage. Water level in the lake was cleterminecI by a lava clam at the outlet (4,138 ft above sea level; USFWS 20021. Even uncler drought conditions, the lake level remained above the level of the natural outlet, except briefly cluring oscillations caused by wind (USFWS 2002). When Link River Dam was constructed, the natural rock clam at the outlet of Upper I(lamath Lake was removed so that the storage potential of the lake couicI be used in support of irrigation. Thus, since 1921, lake levels have varied over a range of about 6 ft rather than the natural range of about 3 ft (Figure 3-21. Drawclown of about 3 ft from the original minimum water level of the lake has occurred in years of severe water shortage (1926,1929, 1992, anti 19941. The operating range of the lake in the context of mean clepth ancI contact between the lake ancI its wetiancis has raisecI numerous questions about the environmental effects of water-level manipulations, especially uncler the most extreme operating conditions (USFWS 20021. The U.S. Bureau of Reclamation (USBR 2002a) has proposed operating Upper I(lamath Lake over the next 10 yr according to guiclelines that reflect recent historical operating practice (Figure 3-2; Chapter 1). The open ques- tion for researchers ancI for the tribes ancI government agencies charged with evaluating the two enciangerecI suckers is whether the USBR proposal for future operations is consistent with the welfare of listecI suckers in Upper I(lamath Lake. In a biological opinion issued in response to USBR's proposals, the U.S. Fish anti WilcIlife Service (USFWS 2002) has concluclecI that operations shouicI involve limits on water levels that are more restric- tive than those proposed by USBR. USFWS has temporarily accepted the water-level criteria proposed by USBR (2002a), but has required a revised approach to predicting water availabilities in any given year (Chapter 11. The USBR 10-yr plan is basecI on a commitment of USBR not to allow Upper I(lamath Lake to fall in any given year below the minimum water levels that were observed in 1990-1999 for four hycirologic categories of years ancI not to allow the interannual mean water levels for these catego- ries to fall below recent interannual means (1990-19991. Figure 3-2 shows the March 16-October 30 operating range basecI on interannual means for each of the four hycirologic categories. The database for the definition of the categories incluclecI water years 1961-1997 (USBR 2002a, p. 391. The calculations were basecI on the outflow from Upper I(lamath Lake for April-September. Years above the mean outflow, which is 500,400 acre-ft, are clesignatecI "above average." Those within one stanciarcI deviation be- low the mean are clesignatecI "below average"; the expected long-term frequency for these years is 34/O (on the basis of a normal distribution. Curve-fitting was not suitable for evaluating years of lower flow, however.

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100 . - ~ . 5- 50 be ~ ~ . = ~ o Cat ^= ~ 2 ~ =~ ~ _ O T ~ o _ aa~deauea~ ~ ~ ~ no 0 LC) ~ A =0 LC) o ~ ~ I I I I T I I Stoat ~ ~ := o ~ o ~ ~ ~ > 0 ~ ~ ad ~ O =~ ~ ~~ ~ a ~ a, ~ a, ~ a, 'M ~ (~d ~ ~ ~ c 2 ~ ~ ~ ,5 ~ a lo' I i 1 1 1 O-e' =) 1 1 1 1 1 1 1 >~= 0 50 cot ~ ~ ~ ~ ~ ~ ~ A ~ ~ ~ ~ ~ ~ ~ ~ 50 (laAarIcaSaAoqV baas) uol~cAal~ao~JmSla~ ~ cd cry .o Em

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES 101 Two extreme years, 1992 anti 1994, were clesignatecI "critical ciry" anti account for about 5/O of the total. By difference, a fourth category, clesig- natecI "ciry," is clefinecI; it accounts for about 1 1% of years. For each category of years, the maximum water levels occur in the spring. Water levels typically begin relatively high as of micI-March anti then rise slightly, after which they fall because of the cumulative effects of cirawclown anti, after rune, the reclucecI volume of runoff (Figure 3-31. Operations for the four hycirologic categories differ most notably in their lower extremes, which occur after luly. In comparison with a baseline condition, which USER defines as lacking I(lamath Project operations but with all project facilities in place, proposed operations typically produce water levels that are above the baseline between March anti the encI of lune anti below the baseline cluring the last half of the summer or fall (USER 2002a). Upper I(lamath Lake receives most of its water from the Williamson River (inclucling its largest tributary, the Sprague River) anti the WoocI River. Aciclitional water sources inclucle precipitation on the lake surface, direct drainage from smaller tributaries anti marshes, anti springs that bring water into the lake near or beneath the water surface. The waters of the lake have only moderate amounts of clissolvecI solicis (interseasonal median, about 100 ~S/cm) anti the same is true of alkalinity (interseasonal median, about 60 mg/L as calcium carbonate). As clescribecI below, the lake is naturally eutrophic, but concentrations of nutrients in the water column may have increased over the last several clecacles. The fish community of the lake couicI be clescribecI as a diverse array of nonnative species superim- posecI on a previously abundant but now reclucecI group of native fishes, 4,144 - 4,143 - 4,142 - 4,141 - 4,140- au au _' ~ 4,137- au au ~ 4,135- 4,139 - 4,138 - 4,136 - 4,134 - -7~( at, ma, . 1 1 1 1 1 1 Jan Feb Mar Apr May Jun Jul 1999 >< 1992 box _, ,,,~. ~ >I _~ ~ Aug Sep Oct Nov Dec FIGURE 3-3 Water level in Upper I(lamath Lake in year of near-average mean water level (1999) and year of extremely low water level (lowest 5%; 1992~.

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102 FISHES IN THE KLAMATH RIVER BASIN most of which are enclemics (Chapter 61. The biota in general has uncler- gone consiclerable change in the last few clecacles. Upper Klamath Lake has several large marshes at its margins. The area of the marshes has been greatly reclucecI (loss of about 40,000 acres from the lake margin; USFWS 20021. The remaining marshes are most strongly connected to the lake at high water anti are progressively less connected at lower water levels clown to about 4,139 ft above sea level, at which point they become clisconnectecI. Poor water quality in Upper Klamath Lake causes mass mortality of listecI suckers anti may suppress the suckers' growth, reproductive success, anti resistance to disease or parasitism. Potential agents of stress anti cleath inclucle high pH, high concentrations of ammonia, anti low clissolvecI oxy- gen (USFWS 20021. Extremes in these variables are explainecI by the pres- ence of clense populations of phytoplankton (primarily the cyano bacteria! taxon Aphanizomenon flos-aq?vae), especially in the last half of the growing season (Kane 1998, Welch anti Burke 20011. Because phytoplankton pop- ulations annually reach abundances exceeding 100 ~g/L of chlorophyll a, the lake can be classifiecI as hypertrophic (or, equivalently, hypereutrophic) according to stanciarcI criteria for trophic classification of lakes (OECD 1982: peak chlorophyll over 75 is hypertrophic). Hypertrophic lakes often show extremes in chemical conditions resembling those observed in Upper Klamath Lake. The main subjects of interest with respect to Upper Klamath Lake proper Miscounting the tributaries, which are clealt with in the next chap- ter) inclucle factors that have been suspected by researchers or by govern- ment agencies of being potentially harmful to the enciangerecI suckers. Where water quality is concerned, the causes of the current trophic status of the lake are of great interest, as is the current predominance of a single algal species, Aphanizomenon flos-aq?vae, in the phytoplankton. Within the suite of variables affected by trophic status, special attention must fall on pH, ammonia, anti clissolvecI oxygen, all of which have the potential to be clirectly or inclirectly harmful to the welfare of the enciangerecI suckers. For all water-quality variables, associations between water level anti water qual- ity are of special interest because USER has the potential to moclify opera- tions so as to control water level. Finally, physical habitat, especially as affected by water level, is of concern anti will be clealt with here. Nutrients ant! Trophic Status of Upper Klamath Lake Nutrient limitation of phytoplankton in lakes usually is seasonal anti almost always is associated with nitrogen, phosphorus, or both of these elements. Typically, phosphorus anti nitrogen are reaclily available cluring winter because clemancI is low. In spring, the most available forms are taken

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES 103 up, ancI nutrient limitation often ensues. If the most reaclily available forms are available in quantities above about 10 ~g/L, there is a strong implica- tion that no limitation is occurring (e.g., Morris ancI Lewis 19881; at lower concentrations, nutrient limitation is possible but may be clelayecI by inter- nal storage. Nutrient limitation often is relievecI in the fall by creep, continu- ous mixing of the water column, cleclining irracliance, ancI lower metabolic rates caused by lower temperatures. Nitrogen limitation can be clefeatecI by some taxa of bluegreen algae ~cyanobacteria) capable of fixing nitrogen (converting N2 to NH31. Nitro- gen gas (N2) is present in consiclerable quantity in water, ancI the overlying atmosphere acts as a large reservoir that can replenish removal of nitrogen gas by nitrogen fixation. The heterocystous bluegreen algae which have a special cell, the heterocyst fix nitrogen reaclily, although the fixation pro- cess requires high intensities of light (Lewis ancI Levine 19841. Heterocys- tous bluegreen algae clo not grow well in some situations, however, for reasons that are only partly unclerstoocI (Reynoicis 19931. Thus, nitrogen clepletion sometimes can occur without inclucing growth of nitrogen fixers. Nitrogen fixers grow well in most warm, fertile waters of high pH. When phosphorus is abunciant in such waters but nitrogen is scarce, nitrogen fixers have a competitive acivantage ancI often become clominant elements of the phytoplankton. This is the situation in Upper Klamath Lake. For the phytoplankton as a whole in Upper Klamath Lake, nitrogen is limiting (see below), but Aphanizomenon has circumventecI nitrogen limitation through nitrogen fixation ancI thus clominates the community. Typically, the most effective way to contro! phytoplankton abunciance in lakes is to restrict phosphorus supply. Restriction of nitrogen supply is not as effective, because it may leacI to the clevelopment of nitrogen fixers that are able to offset restrictions in nitrogen supply. Thus, the most obvi- ous way of attempting to contro! phytoplankton populations in Upper Klamath Lake is to restrict phosphorus supply. As explainecI below, Upper Klamath Lake presents special clifficulties for strategies involving contro! of phosphorus. Phosphorus in Upper Klamath Lake The watershecI of Upper Klamath Lake is geologically rich in phospho- rus (Walker 20011. Springs have a meclian phosphorus content of about 60 ~g/L as soluble reactive phosphorus, which BoycI et al. (2001, citing Walker 2001) take as an estimate of the backgrouncI clischarge-weightecI mean phosphorus concentration. This may be an unclerestimate, given that springs typically have little or no particulate phosphorus or soluble organic phos- phorus, both of which wouicI be present in natural runoff from the water- shecI. In contrast, watershecis of granitic geology often have clischarge-

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104 FISHES IN THE KLAMATH RIVER BASIN weighted mean total P concentrations of 20 ~g/L or less (inorganic P about 5 ~g/L), proviclecI that they are not clisturbecI by human activity (e.g., SchincI- ler et al. 1976' Lewis 19861. Because background concentrations of phosphorus reaching Upper I(la- math Lake are quite high, the lake probably supported clense populations of phytoplankton before lancI-use clevelopment. Early observations indicate that the waters were green, ancI thus eutrophic, at a time when water quality wouicI have been changed little from the natural state. If, as sug- gestecI by BoycI et al. (20011' phosphorus reaching the lake wouicI have hacI originally a clischarge-weightecI mean phosphorus concentration of about 60 ~g/L, phosphorus in lake water wouicI have been somewhat below 60 g/L (because of sedimentation of some phosphorus) in the absence of internal loacling (net increase originating from secliments). On the basis of empirical relationships between chlorophyll a ancI phosphorus (OECD 19821' the mean chlorophyll a in the growing season with total phosphorus at 60 ~g/L wouicI have been in the vicinity of 20 ~g/L, which wouicI have corresponclecI to short-term maximums of 40-60 ~g/L, or about 20% of the current maximums. The concentrations of phosphorus in the lake couicI have been higher, however, if substantial internal loacling from sediments occurred uncler natural conditions, in which case chlorophyll couicI also have been higher. Monitoring of phosphorus entering the lake has shown that the current clischarge-weightecI mean phosphorus concentration in waters entering Up- per I(lamath Lake is near 100 ~g/L, about 40% of which is consiclerecI to be anthropogenic (BoycI et al. 20011. Concentrations in the lake cluring spring are only about 50 ~g/L (BoycI et al. 2001' Figure 2-6; there is consiclerable variation from year to year); the difference between the supply water ancI the concentrations in spring is accounted for by sedimentation of the par- ticulate fraction of incoming phosphorus ancI by mechanisms that convert incoming soluble phosphorus to particulate phosphorus that can undergo sedimentation. The currently observed total phosphorus concentrations in spring, if not supplementecI by any other sources, wouicI support mean algal abundances cluring the growing season corresponding to chlorophyll a at 20 ~g/L or less, according to equations clevelopecI by the Organization for Economic Co-Operation ancI Development ( OECD 19821. When the growing season begins (in about May), Upper I(lamath Lake shows a steady rise in concentrations of total phosphorus culminating in summer concentrations of 200-300 ~g/L (BoycI et al. 2001' Figure 2-6; there is consiclerable variation from year to year). These concentrations greatly exceed the clischarge-weightecI mean concentrations in inflowing water (about 100 ~g/L) ancI also greatly exceed the concentrations in the lake cluring spring (about 50 ~g/L, Figure 3-41. Thus, the great increase in

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES i_ ~ 350- _' o 50 au 300 - 250 - 200 - 150 - 100 - 50 - O- 105 Current Inflow Background Inflow 1 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec FIGURE 3-4 Total phosphorus concentrations in Upper I(lamath Lake during 1997 (an arbitrarily chosen year) and approximate discharge-weighted mean total phos- phorus for inflow for background and for current conditions. Source: Data from Walker 2001. concentrations of phosphorus cluring the growing season must be attrib- utecI to an internal source (secliments). Concentrations of soluble phosphorus in sediments of Upper I(lamath Lake were stucliecI by Gahier anti Sanville (1971), as reported by Bortleson anti Fretwell (19931. Sediment samples taken at one location in 1968-1970 showed a median soluble phosphorus concentration in the interstitial waters of about 7,000 vigil, or about 25 times the maximum concentrations ob- servecI in the overlying lake water (another location showed less extreme deviation from lake water). Thus, for at least some portions of the lake, sediment pore waters contain substantially more soluble phosphorus than the overlying lake water anti can serve as an internal source of phosphorus if the phosphorus leaves the sediments. This is a common situation in fertile lakes. The efficiency with which phosphorus is releasecI from sediments varies greatly according to the conditions in a particular lake. There are four potential mechanisms of release: (1) If the sediments are clisturbecI by wincI- ciriven currents or by other means (organisms or clegassing), interstitial phosphorus can be transferred to the water column simply by agitation. (2) Decrease in the reclox potential (increase in availability of electrons) in the surficial sediments caused by intensive microbial respiration, as wouicI be the case for highly organic sediment, can cause biogeochemical changes that result in acceleratecI release of mineralizecI or soluble organic phospho- rus from the sediments to the overlying water, even if the sediments are immobile. (3) High pH at the sediment surface may cause release of acI- sorbecI phosphorus from sediments, with or without agitation of sediments.

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES 133 ably because it is creeper anti smaller. Aphanizomenon flos-aq?vae probably is present anti apparently creates blooms but not to the same clegree of Upper Klamath Lake (USFWS 20021. Aphanizomenon probably fares bet- ter in this reservoir than in Clear Lake because the latter has more sus- penclecI inorganic turbidity, which shacles the water column. Information on temperature, specific conductance, pH, anti clissolvecI oxygen was collected for the first half of the 1990s by automated monitor- ing anti occasional vertical profiles (USER 2002b), as was the case for Clear Lake. The pH reaches higher extremes than in Clear Lake but is less ex- treme than in Upper Klamath Lake. This probably reflects a gradient of algal photosynthesis across the three lakes. Dissolved oxygen in Gerber Reservoir is substantially clepletecI in creep water both in summer anti in winter, but without any obvious effect on fish. No episodes of mass mortal- ity of the shortnose sucker, which occupies Gerber Reservoir, have been reported. During 1992, when cirawclown of the lake was severe, the lake was aerated (USFWS 20021; sampling inclicatecI that the fish hacI reachecI suboptimal body condition cluring the drought. Uncler other circumstances, the population appears to have been stable in that it has shown no inclica- tion of stress, has preserved a cliversifiecI age structure, anti has been abun- ciant. For reasons primarily having to clo with water quality, the low water levels of 1992 serve as a guideline for setting thresholds to protect the fish from stress. LOWER KLAMATH LAKE Lower Klamath Lake has been reclucecI to a marshy remnant by clewa- tering. It has occasional connection to the Klamath River through which it appears to receive some recruitment of young suckers, but there is no adult population. Water quality apparently has not been stucliecI in any system- atic way. Development of an aclult population is unlikely unless the clepth of water can be increased, which would involve incursion of the boundaries of the lake onto lancis that are used for agriculture. If the lake were cleep- enecI, water quality might be adequate for support of suckers. TULE LAKE Tule Lake historically was very large and capable of supporting, in conjunction with the Lost River, large populations of the shortnose anti Lost River suckers (Chapter 51. It has been reclucecI to remnants as a means of allowing agricultural use of the surrounding lancis. Water reaches Tule Lake from Upper Klamath Lake or from the Lost River drainage via irri- gatecI lancis or from Clear Lake or Gerber Reservoir. Water is removed

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34 FISHES IN THE KLAMATH RIVER BASIN from Tule Lake (now appropriately called Tule Lake Sumps) by Pump Station D (USER 2000a). There are two operational sumps at Tule Lake now: 1A ancI 1B. In the recent past, Sump 1B has been much less likely to hold aclult suckers than Sump 1A; it is shallower ancI has shown a higher rate of sedimentation than Sump 1A. It also appears to have worse water quality than Sump 1A. Sump 1B is being manipulated by USFWS for increase of marshland in the Tule Lake basin. Some water-quality information is available on Tule Lake through monitoring cluring the 1990s (USER 2001a) ancI fish have been sampled (Chapters 5 ancI 61. It appears that the sucker population consists of a few huncirecI inclivicluals, including shortnose ancI Lost River suckers, ancI that these favor specific portions of Sump 1A (the "doughnut hole" or a loca- tion in the northwest corner) that presumably provide more favorable con- clitions than the surrounding area. Monitoring of Sump 1A has not shown any incidence of strongly clecreasecI oxygen concentrations or extremely high pH, as would be the case in Upper I(lamath Lake (USER 2001a). These adverse conditions may occur in Sump 1B, however. The fish of Tule Lake, although not very abundant, appear to be in excellent body concli- tion, ancI this suggests they are not experiencing stress. Suckers migrate from Tule Lake Sumps; migration terminates on the Lost River at the Anderson Rose Diversion Dam (USFWS 2002, Appendix C), in the vicinity of which spawning is known to occur. Water-quality conditions there for spawning appear to be acceptable (USER 2001a). Lar- vae are proclucecI but apparently are not passing into the subaclult ancI adult stages. From the water-quality perspective, it appears that the Tule Lake popu- lation is potentially closer to survival conditions than the Upper I(lamath Lake population. An unresolved mystery, however, is the fate of larvae. It is not clear whether water quality prevents the larvae from maturing, or if other factors are responsible for their loss. Sedimentation threatens the apparently goocI conditions for aclults in Sump 1A. Without aggressive management, the favorable portion of Sump 1A may become progressively less favorable in the future. RESERVOIRS OF THE MAIN STEM There are five main-stem reservoirs (Table 3-11; because Copco 2 is extremely small, it generally cloes not receive inclepenclent consideration. The composite residence time of water in the main-stem reservoirs, which extend about 64 mi from Link River Dam to Iron Gate Dam, averages about 1 mot At moderately low flow (for example, 1,000 cfs), hydraulic residence time is close to 2 ma; ancI at moderately high flow (such as 6,000

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES 135 cfs), it is close to 10 clays. Thus, some of the processes that wouicI make these lakes distinctive from each other ancI from their source waters are not expressed because of the relatively rapicI movement of water through the system. The main source of water for the main-stem reservoirs is Upper I(la- math Lake, but it is not the only source. Agricultural returns ancI drainage water enter the system upstream of the I(eno Dam (Figure 1-2) by way of the I(lamath Strait Drain (about 400 cfs, summer) anti the Lost River Channel (about 200-1,500 cfs, fall ancI winter). In aciclition, coicI springs provide about 225 cfs all year at a point just below the t.C. Boyle Dam; ancI two tributaries, Spencer Creek ancI Shove! Creek, provide 30-300 cfs to t.C. Boyle Reservoir anti Copco Reservoir. Fall Creek anti lenny Creek provide 60-600 cfs to Iron Gate Reservoir. During the wet months, sources other than the Link River, which brings water from Upper I(lamath Lake, provide about one-thircI of the total flow reaching Iron Gate Dam; in midsummer, these sources may account for up to 50/O of the total water reaching Iron Gate Dam (PacifiCorp 2000, Figure 2-71. Thus, source waters of diverse quality influence the quality of water in the reservoirs. The waters of Upper I(lamath Lake often bring large amounts of algal biomass to the upper encI of the system, along with large amounts of soluble ancI total phosphorus. When Upper I(lamath Lake is experiencing senescence of its algal population, the entering waters also may have low concentrations of clissolvecI oxygen anti an abundance of decomposing organic matter. Irrigation tailwater anti other drainage wouicI carry abundant nutrients ancI couicI carry organic matter but wouicI probably lack substantial amounts of algae. Spring waters ancI tributary waters wouicI be the coolest ancI cleanest of the water sources. The reservoirs cliffer physically in several ways that are likely to influ- ence water quality. I(eno Reservoir ancI t.C. Boyle Reservoir are shallow ancI have the lowest hyciraulic residence times. Physically, they resemble rivers more than lakes. In each, the water is poolecI at the lower encI ancI may run swiftly at the upper encI, thus potentially benefiting from reaeration (gas exchange). The two lower reservoirs are much creeper anti have hy- ciraulic residence times that are short on an absolute scale but much longer than those of the two upper reservoirs. None of the reservoirs has very creep withcirawal. Thus, for the two reservoirs that support stable stratification (Copco anti Iron Gate), with- cirawals reflect the characteristics mostly of epilimnetic (surface) water' although their withcirawal cone may extend a short distance into the hypo- limnetic (creep) zone at times (seas 20001. For example, the temperature of water leaving Iron Gate Dam cluring midsummer, when the hypolimnion has a temperature of about 6C, reaches 22-23C (PacifiCorp 2000, Figure 4-5; Deas 2000, Figure 6.5) because the powerhouse withcirawal is at about

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136 FISHES IN THE KLAMATH RIVER BASIN 12 m clepth when the lake is full. For Copco, withcirawal is at about 6 m when the lake is full. Thus, coicI hypolimnetic water of the two deepest reservoirs tencis to be much more static hyciraulically than the upper water column cluring the stratification season, as wouicI be the case in a natural lake of similar depth; the main withcirawal occurs by way of the epilimnion. A small withcirawal (about 50 cfs) for the Iron Gate Hatchery cloes occur from the hypolimnion at Iron Gate Reservoir, however. The quality of water in the reservoirs ancI leaving the reservoir system has been stucliecI many times by numerous parties ciating back to the 1970s. PacifiCorp has sponsored a number of studies in conjunction with its FecI- eral Energy Regulatory Commission (FERC) licensing ancI other regulatory requirements, ancI USER has sponsored studies of water quality because of its oversight responsibilities for the I(lamath Project. The city of I(lamath Falls has also stucliecI water quality, particularly in the upper encI of the system, ancI the Oregon Department of Environmental Quality has stucliecI ancI analyzecI water quality from the viewpoint of fisheries. Other informa- tion is available from the U.S. Geological Survey, the U.S. Army Corps of Engineers, ancI the North Coast Regional Water Quality Control Board. In its consultation document on FERC relicensing, PacifiCorp (2000) provides an overview of the monitoring programs. Monitoring to ciate provides useful information but shows several clefi- ciencies. Most of the monitoring has been limitecI to water-quality variables that can be measured with meters (temperature, pH, specific conductance, ancI clissolvecI oxygen). There is much less information on nutrients, total phytoplankton abundance, phytoplankton composition, total organic mat- ter, ancI other important variables. Thus, interpretations are necessarily limitecI in scope. Also, there have been few efforts to synthesize ancI inter- pret the data, most of which exist merely as archives. Hanna ancI Campbell (2000) have moclelecI temperature ancI clissolvecI oxygen in the reservoirs. The temperature mocleling is useful for planning, but the oxygen mocleling fails to incorporate primary production, which couicI be important. Deas (2000) has clone extensive mocleling for Iron Gate Reservoir that is espe- cially useful for temperature ancI clissolvecI oxygen. A full, system-level unclerstancling of the reservoirs is not yet available, however. During the coo! months (October or November through May), all the lakes are isothermal ancI appear to mix with sufficient vigor to remain almost uniform chemically (see, for example, Figure 3-131. During the warm season, there may be substantial differences in temperature ancI wa- ter quality with depth. I(eno Reservoir ancI t.C. Boyle Reservoir are not creep enough to sustain thermal stratification cluring summer. They may stabilize briefly, however, in which case oxygen may be clepletecI from creep water (see Figure 3-14), but such clepletions probably are interrupted by episodes of mixing. Copco ancI Iron Gate reservoirs, in contrast, stratify

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES Copco, January O - 5 - 10- 15- a' 20- 25 - 30 - o 4 8- 12- 16- 20- 24 - 28 - 32 - 36 - 0 2 4 6 8 10 4 h X DO, mg/L Temperature,C o 2 4 Iron Gate, January 6 8 : 12 14 ! 10 12 Temperature,C ~ 137 DO, mg/L ! FIGURE 3-13 Water temperature and dissolved oxygen (DO) in Copco and Iron Gate Reservoirs, January 2000. Source: Data from USBR 2003. stably on a seasonal basis. Thus, the water near the bottom of these two reservoirs can be classifiecI as hypolimnetic ancI has a much lower tempera- ture than that of the upper water column. As expected, oxygen is clepletecI in the hypolimnion of both lakes. Although the rate of oxygen clepletion varies across years (seas 2000), both reservoirs apparently have an anoxic hypolimnion for as much as 4 or 5 ma beginning in the last half of summer. Periodic episodes of severe oxygen clepletion may occur in the upper two reservoirs. One such event appears to have occurred in 2001, when the entire water column of I(eno Reservoir became hypoxic or anoxic (Figure 3-151. It is not known how often such an event occurs. Because no mass mortality of fish in the reservoirs have been recorclecI, it is possible that the

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138 to- . au ~ 3- 2 - 4 - 5 - 2 3 - 4 - 5 - 6 - 7 - 8 - O - ~ 5 ~ 10 :5 15 20 30 5 10 15 20 25 30 35 40 FISHES IN THE KLAMATH RIVER BASIN Keno, July 0 5 DO, me : 10 15 20 25 O Temperature,C 1 0 5 J.C. Boyle, July 10 15 20 25 ~ T DO, mg/L Copco, July 0 5 10 15 Temperature,C ~ ~ ' f - DO, mg/L ~ Temperature,C - - > - Iron Gate, July 0 5 10 15 20 ' f Temperature,C 20 25 25 30 3 ' DO, ma: - FIGURE 3-14 Water temperature and dissolved oxygen (DO) in all main-stem reservoirs, July 2000. Source: Data from USER 2003.

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES '_ ~ au ~ 4 139 1 1 1 1 , . / Temperature ~ I 234 236 238 240 242 244 River Miles l l 246 248 1 1 250 252 234 236 238 240 242 River Miles Dissolved Oxygen 1 244 246 248 250 252 FIGURE 3-15 Longitudinal transect data on I(eno Reservoir (Lake Ewaunal, 13- 14 August 2001. Isolines indicate temperature at 1C intervals (top panel, increas- ing from 18C) and dissolved oxygen at intervals of 1 mg/L (bottom panel, increas- ing from 1 mg/L). Darker tones indicate lower temperature or lower dissolved oxygen; the darkest zone on the bottom panel indicates concentrations of dissolved oxygen below 1 mg/L (i.e., without or almost without oxygen). Source: Data from USBR. fish uncler these circumstances seek inflowing water of high oxygen concen- tration to sustain them until the episode dissipates. Although the reservoirs receive abundant supplies of algae from Upper I(lamath Lake, they clo not appear to sustain such high rates of algal growth as Upper I(lamath Lake, as incTicatecT by comparisons of pH. Upper I(la- math Lake shows extremes of pH extending above 10, but such extremes are not characteristic of the reservoirs. For example, monitoring of Copco, Iron Gate, ancT t.C. Boyle reservoirs in 1996-1998 byPacifiCorp showed the highest pH to be about 10.0, ancT even this was quite unusual (PacifiCorp 2000, Figure 4-101. More recent ciata are similar in this respect (Table 3-31. Concentrations of phosphorus (means) tencT to be about the same in the main-stem reservoirs as in Upper I(lamath Lake. There is ample phos-

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140 FISHES IN THE KLAMATH RIVER BASIN TABLE 3-3 Summary of Grab-Sample Data for Surface Waters in the Main-Stem Reservoir System, 2001a Concentration, ~g/L Chlorophyll a Location pH NH4+-N NO3--N SRP Total pb 2001 2000 I(eno (1 m) Mean 7.50 1,080 80 160 390 62 - Max 8.82 1,220 90 240 730 - - J.C. Boyle (1 m) Mean 7.31 190 1,120 250 260 50 5 Max 7.86 260 1,760 290 450 - 20 Copco (1 m) Mean 7.91 90 620 150 280 5 10 Max 8.90 130 880 220 560 - 31 Iron Gate (1 m) Mean 8.28 260 370 160 180 5 11 Max 9.45 260 630 280 410 - 46 Below Iron Mean 7.87 80 980 170 190 4 - Gate (0.s m) Max 8.68 90 1,710 210 360 - - aN = 4 in most cases (monthly, June-September); N = 1 for chlorophyll in 2001 (July); additional chlorophyll data for 2000 (N = 6) are shown for three of the reservoirs. Chloro- phyll shown at concentrations below about 20 ~g/L is only a rough approximation because of . . . . . . Imitations on ana yt~ca sensitivity. bTotal P less than SRP (soluble reactive P) for some dates. Sources: USER 2003; PacifiCorp, unpublished data, 2001. phorus in available form for stimulation of phytoplankton growth, but it is not clear whether a net accumulation or a net loss of phytoplankton biomass occurs in the reservoirs because information on phytoplankton biomass shows some internal inconsistencies. Observations from the fielcI suggest that substantial blooms of Aphanizomenon occur in both Copco ancI Iron Gate reservoirs (USFWS 20021. This wouicI not be surprising, given the strong seecling of these reservoirs with Aphanizomenon from Upper I(lamath Lake ancI the presence of large amounts of nutrients. Although the residence times for the two large reservoirs are not great enough to allow the establishment of large populations of algae starting from a very small inoculum, a large inoculum couicI clouble several times over the duration of residence in the two reservoirs ancI thus generate a bloom. Alternatively, a bloom couicI simply be transferred from Upper I(lamath Lake. The clifficulty with the observations, however, is that they are not confirmed by monitoring ciata in 2000 ancI 2001. For both of those years, analysis of chlorophyll a showed abundances of algae ranging from low to high but not extreme in the sense of Upper I(lamath Lake (Table 3-31. There are several possible explanations. FielcI reports might be biasecI by appearance of some algae at the surface while unclerlying populations are not extraorclinarily high. There couicI be something wrong

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES 141 with the chlorophyll analyses, or perhaps large blooms occur very selclom. These matters are unresolvecI. One special concern with respect to coho salmon anti other salmonicis in the I(lamath River main stem is the condition of water as it leaves Iron Gate Dam. Oxygen concentrations below Iron Gate Dam are seasonally below saturation but generally exceed 75/O of saturation (seas 2000), have a temperature that reflects surface waters in the lakes, anti have lower concentrations of nutrients anti algae than would be typical ot upper ~ia- math Lake. Because there is some question about the consistency of ciata on algae, however, no firm conclusions are possible about the export of Apha- nizomenon to the main stem via Iron Gate Dam. . . . . ~ . It appears that the upper two reservoirs have the poorest water quality, as jucigecI from concentrations of nutrients anti clissolvecI oxygen. The two lower reservoirs, although they clevelop anoxia in creep waters cluring sum- mer, maintain better water quality than the upper two reservoirs in their surface waters. The major question of Aphanizomenon blooms in the sys- tem seems unresolvecI because of internal inconsistencies in the data. In general, the water-quality environment seems to be comparable with or slightly better than that of Upper I(lamath Lake in the two upper reservoirs, which may have very low clissolvecI oxygen but clo not seem to have the pH extremes that Upper I(lamath Lake cloes. The two lower reservoirs appear to have better quality overall than the two upper reservoirs, although their creep waters are essentially uninhabitable for fish cluring the summer months because of their lack of oxygen. More synthetic work on the reservoirs is neeclecI. CONCLUSIONS 1. Water-quality conditions in Upper I(lamath Lake are harmful to the enciangerecI suckers. Mass mortality of large fish is caused by episodes of low clissolvecI oxygen throughout the water column. Very high pH anti high concentrations of ammonia, although more transitory than the episodes of low clissolvecI oxygen, may be important agents of stress that affect the health anti body condition of the fish. 2. Poor water quality in Upper I(lamath Lake is caused by very high abundances of phytoplankton, which is clominatecI by Aphanizomenon flos- aquae, a nitrogen fixer. Suppression of the abundance of Aphanizomenon is essential to the improvement of water quality. 3. Very high abundance of Aphanizomenon in Upper I(lamath Lake is almost certainly caused by human activities, but mechanisms are not clear. One hypothesis is that increased algal abundance has occurred because of an increase in phosphorus loacling in the lake. An alternative hypothesis, which is more consistent with the shift in dominance to Aphanizomenon

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42 FISHES IN THE KLAMATH RIVER BASIN anti with the naturally rich nutrient supply of phosphorus to the lake, is that loss of wetiancis anti hycirologic alterations have greatly reclucecI the supply of limnohumic acids to the lake. According to this untested hypoth- esis, loss of limnohumic acids greatly increased the transparency anti may also have reclucecI inhibitory effects caused by the limnohumic acids. These changes allowecI Aphanizomenon to replace diatoms as dominants in the phytoplankton. Total phytoplankton abundance then increased because of the ability of Aphanizomenon to offset nitrogen clepletion by nitrogen fixa- tion, which diatoms couicI not clot 4. Substantial evidence indicates that adverse water-quality conditions are not relatecI to water level. Further stucly extenclecI over many years may ultimately show multivariate relationships that involve water level. Control of water quality in Upper I(lamath Lake by management of water level, within the range of lake levels observed cluring the l990s, has no scientific basis at present. 5. Suppression of algal abundance in Upper I(lamath Lake couicI in- volve drastic reduction in external phosphorus loacI or reintroduction of a substantial limnohumic acicI supply, clepencling on the mechanism by which Aphanizomenon has become dominant. Both of these remeclial actions, if undertaken on a scale sufficient to suppress the abundance of Aphanizo- menon, couicI be achieved only over a period of many years anti couicI prove to be entirely infeasible. 6. Because remecliation of water quality in the near term seems very unlikely, recovery plans for the enciangerecI suckers in the near term must take into account the potential for continued mass mortality of suckers. 7. Use of compressed air or oxygen to offset oxygen clepletion near the bottom of Upper I(lamath Lake has been suggested as a means of moclerat- ing mass mortality of aclult suckers. Such a technique cannot be expected to offset oxygen clepletion throughout the lake, but it has some potential to provide refuge zones. The enciangerecI suckers may be particularly well suited for this type of treatment because the large suckers, which are sus- ceptible to mass mortality, congregate in known locations. 8. Researchers have proviclecI a great clear of useful information relatecI to water quality of Upper I(lamath Lake. Needs for aciclitional information inclucle studies clesignecI to show the mechanism for Aphanizomenon cleath; physical studies, inclucling continuous monitoring of temperature anti oxy- gen anti associated analytical anti mocleling work, that demonstrate more clefinitively the mechanisms that promote alternation of stratification anti clestratification cluring the growing season for the lake; studies of the effects of limnohumic acids on Aphanizomenon anti of the former limnohumic acid supply to the lake; studies of clie! pH cycling in the lake; anti studies of water quality uncler ice.

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CURRENT STATUS OF AQ UATIC ECOSYSTEMS: LAKES 143 9. Clear Lake anti Gerber Reservoir lack extremes of pH, oxygen cleple- tion, anti algal blooms that occur in Upper I(lamath Lake. Better water quality, in combination with other favorable factors given in more cletail in Chapters 5 anti 6, appear to explain steady recruitment, diverse age struc- ture, anti goocI body condition of these populations. Deterioration of body condition of the listecI suckers at a time of extreme cirawclown provide a rationale for the lower allowable threshoicis of water level in these lakes. The lakes anti their tributary spawning areas have exceptional value for protection against loss of the two enciangerecI sucker species. Aciclitional studies of limnological variables (ancI those of fish populations) have spe- cial value for use in comparison with water quality anti population charac- teristics of suckers in Upper I(lamath Lake. 10. Tule Lake, which supports suckers in goocI body condition but cloes not show evidence of successful recruitment, may have water quality that wouicI allow recovery of this subpopulation if problems involving spawning habitat anti larval survival were resolvecI. Lower I(lamath Lake, which now lacks aclult suckers, might well support a sucker population if water levels were raised. 11. Of the four major main-stem reservoirs, I(eno ancI t.C. Boyle ap- pear to have the poorest water quality because they are shallow, have the strongest influence from Upper I(lamath Lake, ancI show the least benefit of clilution by waters entering from other sources. Copco anti Iron Gate reser- voirs have better water quality but clevelop anoxia in hypolimnetic waters cluring summer. Water releasecI to the I(lamath main stem from Iron Gate Dam often is below 100% saturation with oxygen but selclom less than 75/0 of saturation ancI may be excessively warm in summer for salmonicis because it is drawn mostly from the epilimnion. Algal populations in Iron Gate Reservoir appear not to reach the extremes that are typical of Upper I(lamath Lake.