It rises in the San Juan Mountains southeast of Telluride and flows northwest, along the southern slope of the Uncompahgre Plateau, past the towns of Placerville and Nucla and joins the Dolores in western Montrose County approximately 15 miles (24 km) east of the state line with Utah.

[3] The San Miguel varies in gradient, from extremely steep in its upper reaches (forming a shallow, rocky, unnavigable stream) to more mellow in the lower sections (30–50 feet per mile (5.7–9.5 m/km) of drop, which offers the whitewater boater a variety of runs all within the class II+--III range).

[3] The preserved zone hosts a riparian habitat, featuring the typical vegetation such as grey alders and narrowleaf cottonwood.

[4] Minimum suggested flows for small vessels is 250 cfs, with the river near Placerville usually becoming navigable in late April or early May.

Other popular outdoor activities at San Miguel River include walking, hiking and fly fishing, for which the conditions are best from July to September.