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3 This report is one of two reports that address the results of the 7-year research program. This report focuses on the analysis and integration or biological, hydrologic, and geomorphological data to .. determine flow needs of the endangered fish species. A companion report, to be produced in 1999, . will compile and synthesize all results from the 7-year research program not covered in this document. The companion report will specifically address issues such as contaminants, propagation, nonnative species control, and fish-passage needs. RESULTS OF THE 7-YEAR RESEARCH PERIOD The San Juan River is similar to other Upper Colorado River Basin (Upper Basin) streams, primarily .i. the Green and Colorado rivers, in that they are all large rivers with high spring flows and low baser l flows, they are all fairly turbid most of the time, they typically have sand and cobble substrate, and they are all subject to late summer and fall thunderstorm activity. The San Juan River is also similar to other portions of the Upper Basin in that it once supported populations of Colorado squawfish and .," razorback sucker that have declined after the completion of major dams. However, the San Juan River is different than the Green and Colorado rivers primarily because it has a steeper overall slope, a higher overall sediment concentration, and more late summer and fall flood events. No wild razorback sucker were found in the San Juan River during the research period, and the Colorado squawfish population appears to be smaller than 100 individuals. Navajo Dam began affecting flows in the San Juan River in 1962, and post-dam flows had lower spring flows and higher late Summer, fall, and winter flows than occurred during pre-dam periods. The advent of research flows in 1992 " to 1997 produced flows more typical of the pre-dam era. . Habitat needs of the two endangered fishes in the San Juan River involve a complex mix of low velocity habitats such as eddies, pools, and backwaters adjacent to swifter tun and riffle habitats. Habitat use changes with time of year and activity (I.e., spawning, feeding, nursery areas, etc.). A natural hydrograph, in terms of peak spring flows and late summer base flows, is important to not only provide the proper habitats at the correct time, but also to provide natural temperatures and productivity cycles for those habitats. Two key habitats important to Colorado squawfish and other native species that were used extensively in the flow recommendation process were cobble bars and backwaters., Cobble bars are spawning areas for Colorado squawfish, and the fish appear to have fidelity for a certain area of the San Juan River called "the Mixer" for spawning. In the Green River, similar fidelity to spawning areas is seen for both Colorado squawfish and razorback sucker. An important feature of Colorado squawfish spawning bars is that the cobbles are very clean with relatively little fine sediments between individual cobbles. These types of areas are more rare in the San Juan River, as well as in other Upper Basin rivers, than just a typical cobble bar. Backwaters are an important habitat for young native fishes, including Colorado squawfish. During studies of young stocked Colorado squawfish in the San Juan River, the fish were found in backwaters 60% of the time, but they were found in other low velocity habitars nearly 40% of the ,liiiiiii ,:\ 1 SJRIP Biology Committee 16 September 1998 8-2 Executive Summary Draft Aow Report . ~