The Klamath River is a major river in northern California and southern Oregon. Iron Gate Dam divides the river into the two subunits where there is a significant change in utilization of the river. Downstream of Iron Gate Dam, the river is very important for the propagation of salmon. To address concerns relating to substrate conditions in the mainstem Klamath River below Iron Gate Dam, the Arcata, California, office of the U.S. Fish and Wildlife Service contracted with the U.S. Geological Survey (USGS) to determine flushing flows required to improve and maintain quality spawning and rearing habitats for salmon, and to reduce the abundance of preferred habitats of the polychaete worm suspected of being the intermediate host for Ceratomyxa shasta, a species of bacteria that infects fish. Historically, the river has had the capacity to move sediment just below Iron Gate Reservoir, but there have been periods when the capacity was very low. The results indicate that if the future is more like the pre-1961 period (low transport capacity) than the more recent period, there will be significant sediment issues in the Klamath River below Iron Gate Dam. It seems that during normal or wet years, winter months, and periods of high flow, sediments are flushed either downstream or deposited on higher surfaces. The recent drought conditions during 2000-2005 probably resulted in extensive fine-grained sedimentation along the river, which in turn may have caused increased establishment of aquatic vegetation and increased concentrations of C. shasta. It appears that releases from Iron Gate Dam as far downstream as Seiad Valley are important in maintaining flow conditions to flush the fines and clean the gravels in the river during summer months, or during drought years. Sediment transport studies indicate that supplemental flows during dry or drought conditions may provide some flushing flows in reaches downstream of the dam. For purposes of flushing fine sediments during drought years or dry summer months, flows in the range of 2,500-5,000 cubic feet per second during a period of days may be necessary. Providing these types of flows in a manner similar to a storm pulse would provide the best opportunity to flush the fines and clean some of the gravels given the upper ranges of flows are achieved.