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STUDY AREA The San Juan River is the southern-most major tributary of the Upper Colorado River Basin. It drains portions of New Mexico, Colorado, Arizona, and Utah. The San Juan River originates in the San Juan mountains of southern Colorado and enters the Colorado River at what is now Lake Powell (Figure 1). Tributaries (Figure 2) include the Animas, La Plata, and Mancos rivers as well as many smaller tributaries such as Montezuma and McElmo Creeks. Navajo Dam, completed in 1962, near Archuleta, New Mexico regulates the flow of the San Juan River. As is typical of tailwaters below large dams, the river downstream of Navajo Dam is too clear and cold to support populations of endangered fish. These cold waters extend some 43 miles downstream to Farmington, New Mexico. Therefore the native-fish study area begins at Farmington and ends at Clay Hills Landing near lake Powell, 176 river miles (RM) downstream. The system of river miles, places RM 0.0 at Piute Farms Marina where the San Juan River joins lake Powell, and proceeds upstream to Navajo Dam (RM 221.8). For data analysis, the study area was stratified into seven river reaches. The seven river reaches are: Reach I-Farmington, NM to Hogback Diversion (RM 179.0 to 158.6), Reach II-Hogback Diversion (NM) to Shiprock, NM (RM 158.6 to 147.9), Reach III-Shiprock, NM to Four Corners Bridge (RM 147.9 to 119.2), Reach IV-Four Corners Bridge to Aneth, UT (RM 119.2 to 101.0), Reach V-Aneth to Bluff, UT (RM 101.0 to 76.4), Reach VI-Bluff to Mexican Hat, UT (RM 76.4 to 53.0), and Reach VII-Mexican Hat, UT to Clay Hills Boat Landing, UT (RM 53.0 to 2.9) (Figure 3). Five man-made diversion structures, located between Farmington, NM and the Colorado state line, may be barriers to fish passage at certain flows (Figure 3). Of these, the concrete weir downstream of Fruitland, NM probably is the greatest obstacle to fish passage. There are no water diversion structures on the San Juan River in Colorado or Utah. Starting at Navajo Dam the river gradient is moderate and the channel begins to form secondary and occasional tertiary channels. Between Fruitland, NM (RM 166) and Four Corners Bridge (RM 119.2) the channel forms numerous secondary (side) and tertiary (side) channels in response to moderate gradient and local alluvial geology. It is in this river reach that an area of the river known as the "Mixer" is located. The Mixer extends from RM 133.4 to 129.8. The river channel in these 3.6 miles of river has been relatively stable over the historic record with little variation in the degree of channel braiding. However, certain areas are locally dynamic. The habitat is complex with numerous channels always present. The locally dynamic areas contribute to this complexity. Between Four Corners and Aneth, braiding becomes somewhat reduced, mainly in response to a change in geology and topography, although the river gradient remains about the same as the Hogback to Four Corners reach. From Aneth to just below Bluff, braiding increases somewhat, but not to the same extent as seen above Four Corners. About ten miles below Bluff, the river becomes canyon-bound and remains a single channel with a slope roughly equal to the average slope of the river between Navajo Dam and Lake Powell. 2 I I I I I . I , , 1 I I I t I I 1 I ,