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-, :~ ~ 10 2.0 BACKGROUND ~ ~ The San Juan River sub-basin is the second largest of the three sUb-basins which comprise the Upper Colorado River basin (Figure l). The San Juan River sub-basin drains about 38,000 square miles of southwestern Colorado, northeastern Arizona, northwestern New Mexico, and southeastern Utah. From its origins in the San Juan Mountains of colorado, the San Juan River flows some 31 miles to the New Mexico border, 190 miles westward to the Four Corners area, and thence another 136 miles to Lake Powell. In its upper reaches, the river traverses rugged terrain and has a relatively high gradient. The river emerges from canyon-bound reaches shortly after entering New Mexico and flows through a broad floodplain for much of its course in New Mexico and Utah. About 70 miles upstream of Lake Powell, the river again enters canyon reaches for the remainder of its course. The river is generally restricted to a single channel in canyon portions, but is often divided into several channels in floodplain reaches. The San Juan River has comparatively few perennial tributaries, and most are in upper reaches. Historically, the Pinos, Piedra, Navajo, Animas, La Plata, and Mancos rivers, Rio Blanco, and McElmo Creek were the only perennially flowing tributaries. other streams such as Montezuma and Chinle creeks seasonally_ 'contributed flows. Numerous washes and arroyos also entered the river, but none provided regular flow. Among tributaries, the Animas River contributed the greatest flow. 2.1 FISH FAUNA 2.1.1 Native Fish Fauna Ichthyofaunal surveys of the San Juan basin prior to extensive European settlement were very limited. This work, nevertheless, documented the occurrence of at least eight and possibly nine native fish species (Table 2.l): cutthroat trout, roundtail chub, Colorado squawfish, speckled dace, flannelmouth sucker, bluehead sucker, razorback sucker, and mottled SCUlpin. Based upon two specimens and skeletal remains in Native American middens, bony tail chub may also have inhabited the river. Of these, Colorado squawfish, razorback sucker, and bony tail chub are listed as endangered under the authority of the Endangered Species Act of 1973, as amended. In addition, New Mexico lists roundtail chub as endangered; Colorado classifies the flannelmouth sucker, bluehead sucker, and roundtail chub as species of special concern; and Utah lists the roundtail chub and Colorado River cutthroat trout as sensitive species. Although Colorado squawfish was reported in the San Juan Drainage prior to 1900, the first confirmed records were not until 1936 when three juveniles were captured at Alcove Canyon, Utah.