Sympatric species within a community often compete for limited resources, such as food items and habitat. The reliance by semi-aquatic snakes on resources in both terrestrial and aquatic habitats might influence either the frequency or intensity of interspecific interactions and also cause sympatric species to be disproportionately vulnerable to habitat alterations. To reduce competition, species might partition specific resources. Three watersnake species—Nerodia erythrogaster, N. harteri, and N. rhombifer—occur in the upper-middle reaches of the Brazos River, in central Texas. We examined the nature of coexistence among these watersnakes by (1) identifying habitat features that predicted site-level occupancy, (2) assessing microhabitat selection in relation to features such as riffle presence and canopy closure, and (3) quantifying environmental variables that influenced detection probabilities of the watersnakes. In-stream riffles were important for all three watersnake species at either the site or microhabitat level, or both. These three species of Nerodia appear to partition their habitat, however, because the snakes were distributed differently with respect to microhabitat features such as canopy closure and invasive saltcedar (Tamarix spp.). Regular assessment of the community composition is needed because N. harteri continues to experience local population declines and extirpations. Habitat management, such as the removal of saltcedar and preservation of in-stream riffles, might promote long-term stability in the populations of all three species.