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Klamath Water Users Association
2455 Patterson Street, Suite 3
Klamath Falls, Oregon 97603
541)-883-6100 Fax (541)-883-88e-mail

September 29, 2004

Mr. Bill Hobson
California Regional Water Quality Control Board
North Coast Region
5550 Skylane Boulevard, Suite A
Santa Rosa, CA 95403

Re: Upper Lost River and Clear Lake Reservoir Watershed TMDL Analysis

Dear Mr. Hobson:

On behalf of the Klamath Water Users Association (KWUA), I would like to thank the North Coast Regional Water Quality Control Board (Regional Board) for this opportunity to comment on the Total Maximum Daily Load (TMDL) analysis for, and the proposed removal or delisting of, the Upper Lost River from Californiaís 303(d) list. KWUA is a nonprofit corporation that has represented Klamath Irrigation Project (Project) farmers and ranchers since 1953. Our members include rural irrigation districts and other public agencies, as well as private concerns operating on both sides of the California-Oregon border. KWUA focuses on issues that affect thousands of people dependent on the Project, including farm and ranch families, local businesses, and our rural communities. KWUA and its members also play an important role in Klamath Basin wildlife conservation activities, including efforts to provide environmental water to two national wildlife refuges.

Overview of KWUA Concerns

In general, we support the Regional Boardís proposal to delist the watershed for nutrients and temperature. We prepared this comment document to further focus on three additional, general areas: 1) Assess the reportís characterization of Klamath Project operations and the two sucker species protected under the Endangered Species Act Point that affect those operations; 2) Identify, where possible, other sources of data that might firm up the reportís conclusions; and 3) Identify actions not discussed in the report that demonstrate progress made relative to conditions on important tributaries to Clear Lake Reservoir.


The Upper Lost River watershed includes Clear Lake Reservoir, the streams draining to Clear Lake Reservoir and the Upper Lost River between the Clear Lake Reservoir dam and the Oregon border. Section 303(d) of the Clean Water Act (CWA) requires states to identify water bodies that do not meet water quality standards and then to establish a TMDL for each water body at a level necessary for attainment of water quality standards. The Upper Lost River is on the State of Californiaís Section 303(d) list because of nutrient and temperature impairments on beneficial uses, primarily those related to the warm water fishery. Regional Board staff has completed an analysis of water quality conditions in this watershed. Based on the results of this analysis, the Regional Board proposes delisting the watershed for nutrients and temperature.

Overall, we commend the Regional Board for preparing a report that is both comprehensive and easy to read. The following comments relate to specific areas where we believe additional explanation would further enhance the reportís credibility.

Juniper Management

Juniper encroachment has been identified by many as a key area of concern in Upper Lost River watershed areas. In recent years, agencies and private landowners have taken progressive steps regarding juniper management in uplands areas. The federal Bureau of Land Management, in particular, is to be commended for their efforts to work with ranchers to control invasive juniper growth. It should be noted that Klamath Falls is the home of REACH, one of the few operating juniper mills in the region.

Current Grazing Practices

The report notes that, while grazing has previously adversely impacted aquatic habitat, the U.S. Fish and Wildlife Service (USFWS) believes that current grazing practices have improved and will protect endangered species. We agree, and this observation applies to public management agencies as well as private landowners who are interested in enhancing the entire watershed in ways that also improve water quality. Grazing practices up and down the Lost River and its tributaries have changed greatly in the past 25 years, where a wide variety of site-specific actions have been taken.

To provide a specific example of this, we point to the progressive efforts undertaken by the Byrne Brothers Ranch, a family operation that was established around Clear Lake in the very early 1900s. With headquarters in Tulelake, California, the operation consists of both private land and approximately 100,000 acres of public lands.

Prior to 1950, the Byrne Ranch used herding to move their cattle over a 50-mile circle of public lands during an 11-month grazing season. After 1950, the area was fenced into several pastures and cattle were rotated through these fenced areas.

In the early 1980s, the Byrnes began working with the U.S. Forest Service to increase the number of pastures so that a new rotation system would mimic the original herding regime. By strategically placing 15 miles of fence to create 12 individual pastures, the Byrnes can graze two separate herds in a 5-year rotation system. They have also developed eight solar wells in upland areas to create off-stream watering opportunities. These wells disperse animals more evenly, achieve greater late season grazing use of upland areas, and relieve pressure during the hot summer months. Finally, the Byrnes have removed western junipers from areas that still have adequate understory vegetation and soil depth to respond to such treatment.

The Byrne Brothers Ranch works to achieve three stewardship goals:

  • Manage private lands in conjunction with public lands to enhance the vegetation communities across the entire landscape.
  • Improve the shrub and vegetation component of the upland ranges through juniper removal.
  • Improve riparian systems on public and private lands.

The Byrneís management strategy has improved water quality by increasing vegetation in riparian zones, which increases sediment entrapment. Increased riparian vegetation has also increased shading along stream courses, resulting in cooler water temperatures that are beneficial to native fish populations. Increased forage production on lands cleared of western juniper benefits both livestock and wildlife. The management changes have created a situation that allows the native plant community to take advantage of weather conditions conducive to maximum plant growth, seed production and regeneration.

The Byrne brothers are working closely with the U.S. Forest Service, USFWS, the Natural Resource Conservation Service, Tulelake High School and the University of California Cooperative Extension to monitor riparian improvement and water quality. Key monitoring components include:

  • Monitoring of riparian systems using permanent channel transects and annual stubble height measurements.
  • Recording of stream temperatures to evaluate the effects of increased shading.
  • Riparian habitat monitoring for successful willow regeneration and plant community composition.

The Regional Board report notes that it is necessary to preserve the aquatic habitat from any harmful effects related to land use activities. It further specifies that Willow Creek and its tributaries (primarily Boles Creek) are the only spawning sites for the sucker populations, and that it is especially important to protect valuable properly functioning riparian conditions in this stream.

We suggest that the Byrnes Ė in cooperation with public agencies Ė are already taking the necessary steps towards this end, since Boles Creek and Willow Creek both flow through lands that they manage, and benefit from those management actions.

Reliance on the 2001 USFWS Biological Opinion for Klamath Project Operations

The Regional Board report extensively references (pages 8, 9, 24-28) the biological opinion (BO) prepared by the U.S. Fish and Wildlife Service (USFWS) in 2001 on long-term operations of the Klamath Project. The recommendations of that document, in part, contributed to the curtailment of irrigation supplies out of Upper Klamath Lake in April of 2001. Itís recommendations on proposed lake levels that year have twice been brought into question by the National Research Council Committee on Endangered and Threatened Fishes in the Klamath River Basin.

We have serious concerns about the 2001 USFWS BO, in part because of its treatment of emergent vegetated habitat for suckers. Little information is available on the larval rearing habitats of Clear Lake and Gerber reservoirs and Tule Lake. Marsh and other emergent vegetated habitats are much less extensive in Clear Lake and Gerber reservoirs than in Upper Klamath and Tule lakes although sucker populations, and presumably larval survival, are quite successful in the former two Lost River watershed reservoirs.

Buettner and Scoppettone (1991) and Desjardins and Markle (2000) found larvae predominantly at non-vegetated sites in Clear Lake Reservoir and Copco Reservoir, respectively. Desjardins and Markle (2000) found this to be the case even though vegetated sites made up most of the sampling sites. Nevertheless, USFWS has focused considerable attention on the potential value of marsh and emergent vegetation for larval sucker habitat.

The 2001 BO relies on quantitative relationships between Upper Klamath Lake elevations and current emergent vegetation habitat availability. No such relationships were developed for the other Klamath Project reservoirs where juvenile sucker recruitment appears more consistent that at Upper Klamath Lake, despite limited emergent vegetative habitat. The 2001 BO did not attempt to reconcile these differences among the existing data and thus has not established the necessity of actual habitat values for shortnose and Lost River sucker larval survival.

While the ecological benefits of marshes, wetlands and their restoration are numerous and well documented, the necessity or actual habitat values for sucker larval survival and success remains to be tested and confirmed. While this occurs, other potential actions to recover the sucker populations must be pursued. The 2001 USFWS biological opinion, in our view, epitomizes the inappropriate, singular focus that some place on Klamath Project operations and their relationship with the health of suckers. The Regional Board report, unfortunately, inadvertently supports this philosophy with every reference it makes to the 2001 B.O.

Focus on Habitat Alterations over Other Factors

The report makes repeated references to the 1998 USFWS listing determination for the sucker fish. While that listing identified many factors contributing to the decline of suckers, the Regional Board report repeatedly (see pages 15, 23 and 25) focuses on the USFWS discussion of "habitat alterations", including lack of spawning habitat, "damming of rivers, instream flow diversion, draining of marshes and other forms of water manipulation". Further, the report includes a quote by Dr. Peter Moyle in its conclusion section that seems to be inappropriate. Immediately after noting that Clear Lake Reservoir appears to possess a healthy population of Lost River and shortnose suckers compared to other populations, it includes Moyleís characterization that the suckers "and their principal habitats have been subjected to just about every environmental insult possible, with no end in sight."

By contrast, we could only find one, relatively spiritless reference (p. 24) made to the impact of the sucker snag fishery that was sanctioned by the state of Oregon on the Lost River and which was only terminated in 1987. The Regional Board report does not reveal that researchers from Oregon State University identified the elimination of snag fisheries as the single most important management action affecting sucker populations. This issue is outlined in further detail in Attachment "A", which is testimony presented by fisheries scientist Dave Vogel before a congressional field hearing held in Klamath Falls, Oregon, last summer. Mr. Vogelís testimony specifically addresses this matter below:

"Just prior to the listing of the suckers in 1988, a sport snag fishery was allowed. Before 1969, the fishery was largely unregulated with no harvest limit; in 1969 a generous bag limit of 10 fish per angler was imposed (Golden 1969). During the early to mid-1980s, despite the belief that the numbers of fish were in a state of rapid decline, the State of Oregon still allowed the sport snag fishery. Ultimately, because of increased focus on the status of the sucker populations, Oregon eliminated the fishery in 1987."


"Simply stated, the largely unregulated snag fishery slaughtered the sucker populations. Since the fishery was eliminated in 1987, the two sucker populations dramatically rebounded. The threat was removed and the populations increased ten-fold. But unlike the rationale to originally list the species, the current inflexibility of the Endangered Species Act (ESA) will not account for that major beneficial effect."

and, finally

"At the time of the listings in 1988, the Klamath Project was not identified as having known adverse affects on the sucker populations, yet four years after the listing, using limited or no empirical data, the USFWS turned to the Klamath Project as their singular focus. Paradoxically, since the early 1990s, despite new beneficial empirical evidence on the improving status of the species and lack of relationship with Klamath Project operations, the USFWS became ever more centered on project operations and increased restrictions on irrigators instead of paying attention to more obvious, fundamental problems for the species. This circumstance caused tremendous expense in dollars and time by diverting resources away from other known factors affecting the species."

We believe additional analyses are required to bolster repeated references that "physical impairments" are adversely affecting beneficial uses. The impact of those "impairments" must be objectively assessed and relatively compared to other sucker fish stressors, including the now-terminated state-sanctioned snag fishery, to justify the emphasis they receive in the report.

Klamath Project Operations Influenced by Fish and Farmers

The Regional Board report suggests that irrigation demands override the needs of aquatic species regarding operation of Clear Lake Reservoir, a key component of the Klamath Project. Again, referencing the 2001 USFWS biological opinion, the report notes, "this schedule is driven by irrigation needs, not the needs of aquatic life". While this conclusion might apply to that particular schedule, it should not be construed as representing overall operations of the Klamath Project, whose users are likely subjected to more environmental regulations than any entity in the Klamath River watershed.

The reportís statement is not consistent with the current biological assessment prepared by the U.S. Bureau of Reclamation for 2002-2012 Klamath Project operations. Pursuant to its trust responsibilities and section 7(a)(1) of the Endangered Species Act, Reclamation proposed to exercise its authorities to provide additional benefits to listed species, beyond the requirements of Section 7(a)(2) of the ESA. Reclamation proposed to do more than strictly adhere to the minimum operational regime of the 10-year period. Reclamation also proposed to establish a "water bank" which, through willing buyers and sellers, provides additional water supplies for fish and wildlife purposes and to enhance tribal trust resources. The water bank proposed by Reclamation has been operational since 2002.

Characterization of Kuchel Act

The Regional Board report notes that the Kuchel Act of 1964 "complicates" the management of the refuge. This appears to be a subjective statement, and suggests that the Kuchel Act is somehow a negative law. The Kuchel Act in fact resolved a controversy over whether the "lease lands" would be homesteaded, versus remaining in federal ownership and leased. The dispute was resolved, of course, in favor of continued federal ownership.

Historic Presence of Redband Trout

The report addresses the presence of redband trout in the study area, apparently because a "cold water fishery" is identified as a potential beneficial use in the watershed. While redband trout may be present in the Lost River system in Oregon, its presence in the Clear Lake Reservoir / Upper Lost River watershed "cannot be confirmed". In fact, nine studies of the area failed to identify a redband trout population in the Clear Lake Reservoir watershed. Ultimately, the report concludes that the possibility of this coldwater species should not be used to mandate more stringent water quality requirements "where the natural environment does not support those conditions". It then includes as an appendix a discussion of the natural history and habitat requirements of redband trout. Finally, despite the evidence presented and cited in the report, it suggests that redband trout might exist in the Upper Lost River "if the dams were removed and the natural flow regimes were restored". The report ultimately recommends that the "potential" for redband trout to exist in the absence of dams be explored in an evaluation of the beneficial uses in this watershed.

Despite extensive documentation demonstrating the absence of redband trout in and above Clear Lake Reservoir, the report repeatedly insists that, perhaps, they were once there, and that, perhaps, dam construction rooted them out. We intend to vigorously engage in any future evaluation of dam removal on the Lost River, since Klamath Project stored water provided by dams is so critical to meeting the demands of irrigation, national wildlife refuges, suckers, coho salmon and other fish and wildlife.

Data limitations

The report notes the limitations to the data used in the analysis. We would be happy to provide any assistance we can to help with future data collection, coordination with local landowners, and assessments that might be conducted in the Upper Lost River watershed.


Thank you for your consideration of our comments, which we hope you recognize for their constructive intent. We support the Regional Boardís decision to delist the watershed for nutrients and temperature.

Also, we would like to incorporate by reference into this letter the September 28, 2004 technical comments submitted by Charles H. Hanson, Ph.D, Senior Biologist/Principal for Hanson Engineering, on behalf of Langell Valley Irrigation District.

If you have any questions or comments about our statements, please do not hesitate to call me at 541-883-6100.



Dan Keppen

Executive Director


cc: U.S. Rep. John Doolittle

California State Senator Sam Aanestad

California Assembly Member Doug LaMalfa

Art Baggett, California SWRCB

David Vanít Hoff, Office of Gov. Kulongoski

Dave Sabo, Bureau of Reclamation, Klamath Falls

Modoc County Farm Bureau

Byrne Brothers Ranch





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