The Upper Animas River watershed in southwestern Colorado is located in the San Juan mountains and has been intensively mined. Active mining has essentially ceased but the impact of past mining on the aquatic ecosystem continues. This paper presents initial results from a study to determine the characteristics of the physical habitat for aquatic animals and the sediment characteristics as related to the habitat. The habitat for trout is limited by high streamflows and by winter conditions. Only the winter habitat limits are considered. The characteristics of the sediment in the river limit the winter habitat along with metals within the substrate.