Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery (2003)

Instead of focusing primarily on how water levels and flows affect endangered and threatened fish in Oregon’s Upper Klamath Lake and the Klamath River — which run from the lake in Oregon through northern California before emptying into the Pacific — the federal agencies charged with protecting the fish should focus on other kinds of initiatives, such as removal of migration obstacles, prevention of entrainment by water management structures, improvement and creation of habitat, and reduction of summer water temperatures in tributaries.

Key Messages

• The committee found some proposed actions as given in the 2001 biological opinions to lack substantial scientific support. In their biological opinions of 2002, the listing agencies appear to have resolved this issue either by obtaining concessions from USBR through mechanisms that are generally consistent with USBR?s goal of delivering irrigation water.
• Adaptive management is accepted in principle by the listing agencies but has not been implemented in the Klamath basin for the benefit of the listed species, except as part of the Trinity River Restoration Project.
• Although suckers of all age classes are present in Upper Klamath Lake, population densities of suckers are low, and there are no signs that the populations are returning to their previously high abundance.
• An alternate hypothesis is that an unusual combination of temperature, flow, and migration conditions occurred in 2002, possibly in association with weather that prevented the river from showing nocturnal cooling to an extent that would usually be expected.
• Barriers to passage caused by dams and diversion structures are important to coho salmon. The main-stem dams on the Klamath River block spawning movements, as do Dwinnell Dam on the upper Shasta River and the Trinity River Diversion project on the Trinity River. Dams also have contributed to habitat degradation.
• CDFG has proposed that the shape of the channel in the lowermost reaches of the Klamath main stem changed in 1997?1998 under the influence of high flows, which caused fish entering the river to be unable to proceed upstream under low-flow conditions.
• Causes of extreme temperatures include diversion of cold flows for use in agriculture, flow depletion that leads to warming of cool water, and destruction of riparian vegetation that leads to loss of shading.
• Coho habitat has been seriously degraded in the tributaries. Lack of cover and impairment of substrate through deposition of sediments are common. Woody debris, which is critical as cover for young fish, has largely been lost as a result of human activity. Excessive depletion of flow may separate fish from adequate habitat in the last half of summer.
• Coho salmon, unlike Chinook salmon, remain in freshwater for an entire year, during which they mainly occupy tributaries, where summer water temperatures can be dangerously high.
• Decrease in main-stem temperatures by augmentation of main-stem flows is problematic because augmentation water must be derived from the surface layer of Iron Gate Reservoir, which is very warm in summer.
• During the second half of September 2002, numerous fish died in the lowermost 40 mi of the Klamath River main stem, 150 mi below Iron Gate Dam. Most of the dead fish were adult Chinook salmon that had just entered the lower Klamath River.
• If a lasting change in channel configuration was responsible, recurrence of the episode can be expected with similar low flows in the future. If other factors were responsible, recurrence may be much less likely. It is unclear what the effect of specific amounts of additional flow drawn from controllable upstream sources (waters from reservoirs on the Trinity River or Iron Gate Reservoir) would have been.
• Information collected through monitoring and research has been valuable, but the absence of an integrated, evolving management plan connected to monitoring, research, review, and periodic readjustment of management actions will hamper progress in the future.
• Mass mortality of large fish in Upper Klamath Lake has occurred for many decades, but anthropogenic factors, especially those leading to strong dominance of Aphanizomenon, probably have increased its severity and frequency. Poor water quality may also challenge the sucker populations in other ways. High pH, for example, could be harmful to young fish even if they are not subject to the mass mortality of larger fish.
• No obvious explanation of the fish kill based on unique flow or temperature conditions is possible.
• Nonnative fishes, which are diverse and abundant in Upper Klamath Lake, may be suppressing the populations of endangered suckers there, but no practical mechanisms for reducing their abundance are known.
• Reservoirs of the main stem Klamath have created new habitat capable of holding endangered suckers, but recruitment of young fish has not been observed. Reservoirs have low potential to support self-sustaining populations.
• The fish kill, although important for Chinook salmon, did not involve many coho salmon (about 1% of the total dead fish) because coho enter the river later than Chinook, and thus were mostly absent when conditions leading to mass mortality occurred.
• The immediate cause of death was massive infection by two types of pathogens that are widely distributed and generally become harmful to fish under stress, particularly if crowding occurs.
• The most important cause of impairment of coho salmon probably is excessively high summer temperatures in tributary waters.
• There is no evidence of a causal connection between water level and water quality or fish mortality over the broad operating range in the 1990s, the period for which the most complete data are available for Upper Klamath Lake. Neither mass mortality of fish nor extremes of poor water quality shows any detectable relationship to water level.