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3 EVALUATION OF THE BIOLOGICAL OPINION ON KLAMATH BASIN COHO SALMON

Coho salmon enter the main stem of the Klamath River for spawning typically in their third year, primarily between October and December. Over most of this interval, main-stem flows below Iron Gate Dam often are high (about 2,500–3,000 cubic feet per second) (NMFS 2001). Thus, standard methods for observing and counting spawning fish are not easily applied, and the size of the spawning population is unknown. Approximations suggest that the entire ESU has about 10,000 spawning coho salmon of nonhatchery origin per year (Weitkamp et al. 1995). Only a small portion of that number is associated with the Klamath Basin, where several important tributary runs have been reduced to a handful of fish (NMFS 2001).

Spawning coho in the Klamath Basin are restricted to use of tributaries that they can reach from the main stem up to Iron Gate Dam. Original spawning runs probably were largest in large tributaries but currently are restricted mainly to numerous small tributaries entering the main stem directly (Yurok Tribe 2001, as cited in NMFS 2001). Large tributaries have been severely degraded, show excessively high temperatures, and are dammed in critical places. Although a minor amount of spawning may occur in the main stem, the main stem serves adults primarily as a migration route.

Fry appear in late fall or winter, when water levels are highest. Most fry probably remain in the tributaries but some move or are swept into the main



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Page 21 3 EVALUATION OF THE BIOLOGICAL OPINION ON KLAMATH BASIN COHO SALMON Coho salmon enter the main stem of the Klamath River for spawning typically in their third year, primarily between October and December. Over most of this interval, main-stem flows below Iron Gate Dam often are high (about 2,500–3,000 cubic feet per second) (NMFS 2001). Thus, standard methods for observing and counting spawning fish are not easily applied, and the size of the spawning population is unknown. Approximations suggest that the entire ESU has about 10,000 spawning coho salmon of nonhatchery origin per year (Weitkamp et al. 1995). Only a small portion of that number is associated with the Klamath Basin, where several important tributary runs have been reduced to a handful of fish (NMFS 2001). Spawning coho in the Klamath Basin are restricted to use of tributaries that they can reach from the main stem up to Iron Gate Dam. Original spawning runs probably were largest in large tributaries but currently are restricted mainly to numerous small tributaries entering the main stem directly (Yurok Tribe 2001, as cited in NMFS 2001). Large tributaries have been severely degraded, show excessively high temperatures, and are dammed in critical places. Although a minor amount of spawning may occur in the main stem, the main stem serves adults primarily as a migration route. Fry appear in late fall or winter, when water levels are highest. Most fry probably remain in the tributaries but some move or are swept into the main

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Page 22 stem, where they can be found in small numbers well into July. Juvenile coho become smolts and emigrate to the ocean between March and mid-June; peak migration occurs in mid-May (NMFS 2001). In general, juvenile coho can be expected to occupy places where summer temperatures are low (12–14°C appears to be optimal for growth). They are also favored by deep pools with complex cover, especially large woody debris, which is essential for survival over winter (Sandercock 1991). Such conditions exist primarily in tributary streams of the Klamath Basin. The reduction in stocks of native coho salmon in the Klamath River Basin has been caused by multiple interactive factors. Drastic reduction in spawning and juvenile habitat has occurred through impoundment and physical alteration of tributaries. Also, large numbers of smolts are released annually from the Iron Gate hatchery. Smolts, which are derived from a combination of Klamath Basin and Columbia River coho, likely compete with or have other negative effects on wild native coho at all stages of their life history, including the smoltification-emigration period, the ocean growth period, and spawning (Fleming and Gross 1993, Nielsen 1994, NRC 1996). Physical habitat in the main stem is a potential concern for the welfare of the coho in several life stages. The spawning run must have adequate flows for passage, which would be impaired by excessively shallow water (e.g., through amplification of predation losses). Access to tributaries is a related consideration for the spawning run, given that little spawning is likely in the main stem. Also, fry that enter the main stem must find cool, well-shaded pools, or return to a suitable tributary. Smolts moving downstream must find suitable temperature, flow, and habitat conditions compatible with their physiological transformation during migration (Wedemeyer et al. 1980). Habitat is an undeniable requirement for all life stages; however, assessment of habitat suitability is difficult and subject to considerable uncertainty. Numerical methods are now being applied to the estimation of habitat area in relation to flow (INSE 1999). These methods are commonly used in evaluating habitat, but in final form they require extensive field measurements that are not yet available. Initial modeling suggests that even though habitat for salmonids increases with higher flows, the percentage increase of habitat space corresponding to increases in flow during dry years is relatively small (INSE 1999, NMFS 2001). Water temperature is a major concern for the welfare of the Klamath Basin coho salmon. Summer temperatures appear to be especially critical. In the nearby Matolle River, which contains coho that are part of the SONCC ESU, the juvenile coho reside almost entirely in tributaries but do not persist when summer daily maximum temperatures exceed 18°C for more than a week

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Page 23 (Welsh et al. 2001). Summer temperatures in the Klamath River mainstem are, as judged by the literature on thermal tolerance, suboptimal or even lethal to juveniles (NMFS 2001). High temperatures are the result of reduced flow in the main stem and in tributaries as a result of diversions, warming of water in lakes prior to its flow to the main stem, and loss of shading. Climate variability, although probably responsible for some interannual thermal variation, is unlikely to be an important factor by comparison with changes in flow and loss of riparian vegetation. Modeling has shown that higher releases of water to the main stem can reduce water temperature slightly (Deas and Orlob 1999) while also reducing the amplitude of daily temperature fluctuations, provided that manipulation of flow itself does not raise the base temperature (see below). It is unlikely, however, that the small degree of cooling that could be accomplished in this way would affect survival of coho salmon because temperatures would continue to be suboptimal. Further modeling is in progress. The biological opinion issued by the NMFS for the Klamath Basin coho salmon states that the Klamath Project harms coho in the Klamath main stem (NMFS 2001). The NMFS presents an RPA with three components: (1) higher monthly minimum flows for the main stem of the Klamath River for April through November as a means of maximizing habitat space in the main stem and suppressing maximum water temperatures, (2) suppression of ramping rates below Iron Gate Dam, and (3) coordination involving other agencies. Figure 6 shows minimum flows given by NMFS as part of its RPA and shows minimum flows proposed by USBR as part of its biological assessment as well as historical low flows in dry and critical dry years (note that in selected months flows can be higher in critical dry years than in dry years because of water management practices). The NMFS RPA proposed low flows are well above historical operating conditions, which in turn are above the minimum flows proposed by USBR. The proposed low-flow limits on the Klamath River might not benefit the coho population significantly. Although the provision of additional flow seems intuitively to be a prudent measure for expanding habitat, the total habitat expansion that is possible with the limited water available in dry years is not demonstrably important to maintenance of the population. In wet years, any benefits from increased flow will be realized without special limits. Year classes that have high relative strength should have emerged from the wet years of the recent past flow regime if flow is limiting. This does not appear to have been the case in the past decade, however. Thus, factors other than dry-year low flows appear to be limiting to survival and maintenance of coho.

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Page 24 Image: jpg ~ enlarge ~ • Dry Water Years, USBR proposed º Critical Dry Water Years, USBR proposed — Mean, 5 Dry Water Years, 1961–1997 –– Mean, 2 Critical Dry Water Years, 1961–1997 Δ NMFS Biological Opinion FIGURE 6 Three flow regimes for the Klamath River below Iron Gate Dam: USBR (2001b, minima for dry and critical years) proposed minimum flows for dry and critical years, historical mean minimum flows for dry and critical dry years, and RPA minimum flows (NMFS 2001). Hydrologic categories used by USBR in its proposals (dry years and critical dry years) are explained in the text. Higher flows might work to the disadvantage of the coho population from July through September if the source of augmentation for flow is warmer than the water to which it is added. Flows in the main stem include not only water passing the Iron Gate Dam but also accruals from ungaged sources consisting of groundwater and small tributaries. Thus, the addition of larger amounts of water from the sequence of reservoirs above Iron Gate Dam might be disadvantageous to the fish. This issue apparently has not yet been studied in any rigorous manner, yet it is critical to the evaluation of higher flows in the warmest months. Increased flows also could have a detrimental effect on the availability of thermal refugia (mainly mouths of small tributaries). Thermal refugia may be most accessible and most extensive at low flows. Increase in flows might reduce the size of these refugia by causing more effective mixing of the small

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Page 25 amounts of locally derived cool water with much larger amounts of warm water from points upstream. Progressive depletion of flows in the Klamath River main stem would at some point be detrimental to coho salmon through stranding or predation losses. Thus, incremental depletions beyond those reflected in the recent historical record could be accomplished only with increased risk to coho salmon. At the same time, the available information provides little support for benefits presumed to occur through the increase of flows beyond those of the past decade. While single-year or multiple-year averages of low-flow extremes beyond those presently reflected in the record cannot be supported, there also is presently little evidence of a scientific nature that increased low flows will improve the welfare of the coho salmon. Modeling of temperature and habitat might be useful, but convincing evidence of a relation between the welfare of the coho and environmental conditions must be drawn to some extent from direct observation. For example, when related to specific flow conditions, year of class strength, abundance of various life history stages, or other biological indicators of success would greatly improve the utility of modeling and other information. The small size and scattered nature of the present native coho population makes collection of such data difficult, however. The RPA requirements related to ramping rates and interagency coordination seem supportable. Given direct field observation of the stranding of coho at the current ramping rates (NMFS 2001) and the mortality that is implicit in these observations, reduction in ramping rates seems a reasonable and prudent measure for protection of coho. Coordination, a final requirement of the RPA, is an obvious necessity because of the need to optimize use of water for multiple purposes.