Biological Opinions - Bureau of Reclamation

11.3.7 Summary of Critical Habitat in Interior-Klamath Diversity Stratum
The current function of critical habitat in the Interior-Klamath Diversity Stratum is degraded
relative to its unimpaired state. Sedimentation, low stream flows, poor water quality, stream
habitat simplification, and habitat loss from poorly designed road crossings plague coho salmon
streams in this stratum. Additionally, critical habitat in the Interior Diversity stratum often lacks
the ability to establish essential features due to ongoing human activities. Water use in many
regions throughout the diversity stratum (e.g., Shasta and Scott rivers) reduces summer base
flows, which limits the establishment of several essential features such as water quantity and
water quality.
11.3.8 Factors Affecting Coho Salmon Critical Habitat in the Action Area
11.3.8.1 Reclamation’s Klamath Project
11.3.8.1.1 Hydrologic Alteration
The Reclamation Act of 1902 (43 U.S.C. 391 et seq.) authorized the Secretary of the Interior to
locate, construct, operate, and maintain works for the storage, diversion, and development of
water for the reclamation of arid and semiarid lands in the western States. Congress facilitated
development of the Klamath Project by authorizing the Secretary to raise or lower the level of
Lower Klamath and Tule Lakes and to dispose of the land uncovered by such operation for use
under the Reclamation Act of 1902. The Oregon and California legislatures passed legislation
for certain aspects of the Klamath Project, and the Secretary of the Interior authorized
construction May 15, 1905, in accordance with the Reclamation Act of 1902 (Act of February 9,
1905, Ch. 567, 33 Stat. 714). The Project was authorized to drain and reclaim lakebed lands in
Lower Klamath and Tule Lakes, to store water of the Upper Klamath and Lost Rivers, including
water in the Lower Klamath and Tule Lakes, to divert and deliver supplies for Project purposes,
and to control flooding of the reclaimed lands.
Starting around 1912, construction and operation of the numerous facilities associated with
Reclamation’s Klamath Project significantly altered the natural hydrographs of the upper and
lower Klamath River. In 1922, the level of Upper Klamath Lake was raised by the Link River
dam. Reclamation’s Klamath Project now consists of an extensive system of canals, pumps,
diversion structures, and dams capable of routing water to approximately 200,000 ac (81,000 ha)
of irrigated farmlands in the upper Klamath Basin (Reclamation 2012).
Hecht and Kamman (1996) analyzed the hydrologic records for similar water years (pre- and
post-Project) at several locations. The authors concluded that the timing of peak and base flows
changed significantly after construction of the Project, and that the operation increases flows in
October and November and decreases flows in the late spring and summer as measured at Keno,
Seiad, and Klamath USGS gage sites. Their report also noted that water diversions also occur in
areas outside the Project boundaries. IGD was completed in 1962 to re-regulate flow releases
from the Copco facilities. However, IGD did not restore the pre-Project hydrograph. Rather,
base flows were altered. Fall flows were slightly increased while spring and summer flows were
228