Habitat assessments were conducted in an intermountain watershed at three spatial extents to explore ways to predict the presence of tubificid oligochaetes likely to support the parasite Myxobolus cerebralis, cause of salmonid whirling disease. Stream reaches with six different reach slope characteristics were selected using GIS. The aquatic habitat in 60 reaches selected at random was measured and classified into distinct habitat units. Within the habitat units, areas of microhabitat with depositional fine sediments were chosen, measured, and core samples were removed to characterize the sediments and benthic oligochaetes. Two tubificids, Tubifex spp. and Limnodrilus hoffmeisteri, were abundant and co-occurred in silt-clay and fine sand sediments in these habitats. Models were posed and tested to predict the presence and relative abundance of tubificids using habitat characteristics from the three spatial extents: reach, habitat unit, and microhabitat. At the reach extent, tubificids were associated with low-reach slope and with slow water habitats. Within habitat units, tubificids were associated with higher percentages of fine sediments and higher stream width:depth ratios. In microhabitat cores, the presence of silt-clay sediments was positively associated with higher average stream width:depth ratios. Since ecological relationships are often scale dependent and stream systems have a natural hierarchy, predictive habitat models such as these that use measures from several scales may help researchers and managers more efficiently identify and quantify aquatic communities at highest risk of infection by the M. cerebralis parasite.