Technical Abstract: The purpose of this investigation was to develop a bed-sediment protocol for discriminating between natural and impacted conditions, based on five designated reaches of the San Juan and Animas Rivers, listed as impaired on the New Mexico 303-d list. A similar analysis was carried out using sixty-five selected gauging stations in the Arizona/New Mexico Plateau Ecoregion (Level III Ecoregion 22), containing the study reaches. Rapid geomorphic assessments and collection of bed-material samples were carried out at 1.5 km intervals over the 110 km length of the San Juan River, at 3 km intervals on the 55 km length of Animas River and near the mouths of major tributaries. The long profile of percent bed-material finer than 2 mm exhibited extremely high values at and downstream of the mouth of Canon Largo. This was interpreted as a large contribution of fine sediment from this source. Other peaks in bed-material percent fines were observed near confluences of Gallegos Canyon, Kutz Canyon, and La Plata River on the San Juan, and Estes Arroyo o n the Animas River, indicating these are also contributors of fine sediment. Hydrological analyses of gauging station data on the San Juan River showed following dam construction in 1962, peak flows had decreases significantly in terms of magnitude and duration. This resulted in reduced sediment-transport capacity, especially in the reach downstream of Canon Largo. The bed material reference value, defined as the median percentage of material finer than 2 mm for stable coarse-bed channels on the San Juan and Animas River is 20.5%, with the interquartile range extending between 12.8% and 29.5%. These values are slightly higher than those for the Ecoregion 22 dataset, being 0.25%, 15.5%, and 21.5%, for the 25th, 50th, and 75th percentiles, respectively.