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001610 .1 Throughout this chapter, references are made to locations in the San Juan River study area, the area between Lake Powell and Navajo Dam. The study area was divided into eight Geomorphic Reaches by Bliesner and Lamarra (2000) (Figure 2.1). Most researchers used the Geomorphic Reaches to organize and analyze their data. In addition, some locations are shown by river mile (RM); RMs were numbered from RM 0 (Piute Farms at the upper end of the San Juan Arm of Lake Powell) to RM 224 (Navajo Dam), and RMs are also shown on Figure 2.1. HABITAT LIMITATIONS Introduction '.'In the San Juan River, habitat may be limiting in a number of ways. Important or "key" habitat . types may be too rare to support sufficient numbers of a species necessary for maintaining a self- sustaining population. Key habitats are those habitats the fishes require, and they are usually identified by comparing use and availability of habitats most-frequently used at various times in the fish's life cycle. Rare habitats that are important to a species are typically key habitats, and as such they may limit the species. Habitat quality may also be too poor to sustain sufficient numbers of a target species. At the onset of the SJRIP, there was a general concern that San Juan River key habitat quantity and quality were low. A basic premise ofthe SJRIP was that reoperation of Navajo Dam to mimic a natural hydrograph would improve both habitat quantity and quality by re- establishing a spring peak and low late-summer, autumn, and winter base flows. It was the consensus of biologists working with the endangered fishes in the Colorado River Basin that natural flow patterns and magnitudes were needed by these fishes (Holden] 979, Minckley et al. 1991, Tyus 1991). The life histories of most native species are integrally tied to the timing, duration, and magnitude of the natural hydrograph. Some species (e.g., razorback sucker) spawn during high spring flows. and their larvae are adapted to utilize habitats that are most available during that time of year. Other species (e.g., Colorado pikeminnow) spawn later in the summer as flows recede, and their larvae utilize habitats that are most available during the low flow periods of late summer and autumn. Chapter 6 of the Flow Report (Holden [Ed.] 1999) discusses the link between the natural hydrograph and the native fishes in more detail. Dams, such as Navajo Dam, alter the natural flow regime in both quantity and timing and, therefore, often have major impacts on the availability of habitat for native fishes (Holden 1979). Native fish specics evolved under certain flow patterns, and a basic hypothesis ofthe SJRIP was that those patterns werc important in providing and maintaining key habitats for these species in the San Juan River. Therefore, the questions that the SJRIP studies were designed to answer were; are there sufficient amounts of key habitat for the two endangered fishes, is the habitat quality sufficient to maintain these species, and will reoperation of Navajo Dam improve key habitat quantity and quality? Also important was the temporal aspect of these questions: as reoperation of the dam continues, how does key habitat quantity and quality vary from year-to-year, from one flow rate to another, and over time? In addition, how are key habitats created, how are they affected by storm events and other natural phenomena, and how are they restored if they become degraded? September 2000 3-2 Program Evaluation Report