Preliminary Aquatic Integrity Assessment for the Lower/Middle Klamath River and the Upper Sacramento River

Executive Summary

August 2004

The Klamath River basin drains approximately 9,691 square miles in southern Oregon and northern California. This river is the second largest in the state of California and historically was the third most productive salmon and steelhead fishery in the continental United States. Since the 1940s, salmon production has dwindled to only 10% of historic levels and 6% of historic coho production.

The Klamath Basin is separated into two sections by four hydroelectric dams. While most of the controversy has focused on the Upper Basin (above Irongate Dam) and water allocations within the Klamath Basin refuge system, the ecological health of the entire Klamath River needs to be assessed from its headwaters near Crater Lake to its mouth in northern California. In particular, far less attention has been directed in assessing health on the mid and lower reaches of the Klamath and how these reaches are fairing ecologically as well as what their restoration needs are in contributing to a systems-wide and holistic approach to restoring the health of the Klamath River. This is especially true given the large fish kill that occurred on the lower Klamath River in 2002.

In November 2002, two science-based conservation organizations, the Conservation Biology Institute (Corvallis, Oregon) and World Wildlife Fund (Ashland, Oregon), conducted an ecological assessment of the mid and lower reaches of the Klamath, including its tributaries and the Upper Sacramento River that flows into the mid Klamath.

Ecosystem health was assessed using computer mapping (Geographic Information Systems – GIS) and satellite interpretation technologies across 870 watersheds; 655 within the mid and lower Klamath and 215 within the Upper Sacramento River. We used a series of indicators or surrogates to assess watershed condition on a relative basis, including road density, stream-road intersections, logging in the basin over a three-decade period, and mining activities.

Because this is the first subbasin assessment of relative ecological condition of the mid and lower Klamath River, this executive summary will focus mainly on the Klamath findings as they are particularly relevant to policy and legislative efforts to manage water uses and restore ecosystem health throughout the Klamath River. In addition, according to monitoring stations of the United States Geological Service, the Klamath is in worse shape today than it was in 2002, the year that 34,000 to 68,000 salmon and trout died from disease in the lower Klamath River due primarily to low water flows and high water temperatures.

Main Findings

• Of the 655 watersheds examined within the Klamath system, 40% were in moderate to very poor condition as determined by well-established surrogates for predicting aquatic ecological integrity, including road density, stream-road intersections, logging in the basin over a three-decade period, and mining locations.
  
• Based on continuing work in the region comparing measurable biological indicators collected at the site level with broader scale predictive models such as the results discussed here, surrogate indicators usually underestimate (i.e., are conservative) the level of aquatic integrity decline that actually exits on the ground.
• Based on this observation, the initial analytical results for the Klamath should be viewed as more sobering than the numbers suggest.
• The scientific literature indicates that when logging exceeds 15-25% of the area of a watershed, ambient and corresponding stream temperatures rise – thus, this is an excellent example of how the condition of the upland systems are inextricably linked with aquatic systems as moderating temperatures can be lethal to salmonids. Because of this fact, including upland management needs to be very much a part of finding a salmon solution as was also indicated by a National Academy of Sciences report on the Klamath River issued in 2003.
• In the area that we examined, 145 watersheds (or nearly ¼ of the entire middle and lower sections of the Klamath Basin) had logging levels already above established thresholds. The heaviest logging occurred in watersheds surrounding the mouth of the Klamath and the North and South forks of the Salmon River.
• In this same area, approximately 23 timber sales totaling 200 million board feet are currently planned in the Klamath-Trinity area of the Klamath National Forest, including logging in unroaded areas and Riparian Reserves (some of which have crossed the established threshold levels).
• Weakening of the Aquatic Conservation Strategy by the Bush administration may push more watersheds above established thresholds by allowing more logging to occur the project level.
• Federal lands are the backbone of salmon production and need to be the core component of the salmon solution. This is especially true as the California Department of Forestry routinely approves timber harvest plans on private lands exceeding 60-85% of the watershed.

In addition, several other factors have contributed to declining health of the river:

• High road densities – 60% of the watersheds were in moderate to very poor condition due to high (>1 mile of road/square mile) road densities.
• High road-stream intersections – approximately 30% of watersheds had moderate to very high levels of road-stream intersections – intersection points act as delivery routes for sediments that degrade water quality and directly damage salmon redds.
• Placer mining – 17% of the watersheds had moderate to very high mining activities (heaviest mining occurring along the mid-Klamath and tributaries, North Fork of Salmon, mid-Trinity, and downstream Shasta and Scott reaches).
• Over allocation of base flows – most low slope gradients (ideal fish habitat) along the Scott and Shasta have been diverted for irrigation, which has fragmented stream connectivity in the tributaries of the Klamath.

This combination of land and water degradations has expressed itself mainly through reduced base flows that impact water quantity and habitat losses that impact water quality throughout the Klamath system. Therefore, approaches that focus only on the Upper Basin are incomplete and will be ineffective in restoring salmon runs on the downstream reaches and tributaries.

System-Wide Protection and Restoration Priorities are Urgently Needed

It is no surprise that the Klamath made the list of most endangered rivers compiled by American Rivers. There are many warning signs that the Klamath system is in a state of disrepair – the most obvious being recent downstream fish kills.

The following seven-point plan needs to be adopted to advance basin-wide recovery:

1. Recognize the Klamath as a total system – restoration and water use needs to be considered from Upper Basin to Mouth particularly how water quantity and quality in upstream reaches affects downstream uses and how improvements to middle and lower reaches can contribute to overall salmon recovery.
2. Prioritize restoration based on comprehensive assessment of river health – mangers need to determine what river reaches would benefit most from road decommissioning, fish migration improvement, and wetlands restoration. According to our analysis, over 415 “restoration” projects are underway on the Klamath but it is unclear whether these projects are strategically aimed at watershed improvements that maximize benefits to salmon and whether they are achieving desired results (need for monitoring).
3. Prioritize fish migration restoration – 36 permanent dams and hundreds of engineered structures and diversions exist from Iron Gate Dam downstream. Many of these can be removed and replaced with more efficient pump delivery systems to meet agricultural demand and permit adult and juvenile fishes to migrate safely through the river corridor.
4. Protect all remaining roadless areas as core salmon refugia and build no new roads – it is especially important to limit and reduce intersections of roads and streams.
5. Reinstate the site level planning components of watershed analysis removed from the Aquatic Conservation Strategy – site level planning allows managers to assess the watershed context of proposed projects. This is especially important in determining whether a particular site is needed for maintaining the functional connectivity of both the aquatic and upland environments influencing salmonids and wildlife.
6. Tighten logging standards at the watershed level especially logging of big trees – timber harvest plans need to be evaluated based on whether they push watersheds above established thresholds particularly within Tier 1 watersheds.
7. Lower demand throughout the system - work with willing private landowners on land acquisitions, conservation easements, and water rights purchasing. This includes restoring or increasing base flows on the Trinity, Scott, and Shasta rivers.

In sum, a comprehensive approach is needed on the entire Klamath that contributes to systems-wide recovery and restoration. This includes demand reduction, lowering impacts on downstream users, restoring and protecting upland ecosystem health, managing national forests for increased salmon production, and restoring historic spawning habitat on the Klamath mainstem and tributaries.

Dr. Dominick A. DellaSala
Director Klamath-Siskiyou Program
World Wildlife Fund
Email: dellasal@wwfks.org

Dr. James Strittholt
Executive Director
Conservation Biology Institute
Email: stritt@consbio.org