The federally endangered watercress darter (Etheostoma nuchale) is restricted to only five springs within the greater Birmingham (AL) metropolitan area. Restricted range, subpopulation isolation and threats from the urban landscape are the major factors endangering the species. The preferred habitat of E. nuchale has been described as the deeper, slow-moving portions of spring pools with dense aquatic vegetation, but its habitat use patterns have not been carefully studied. Because the long-term survival of E. nuchale will likely depend on the protection and restoration of suitable habitat, more needs to be known about its preferred habitats. We studied habitat use patterns of E. nuchale and the geomorphologic and environmental conditions associated with these habitats in Seven Springs, a population recently discovered in 2003. Geomorphology and vegetation were surveyed throughout the spring pool and the spring run connecting it to the nearest tributary. Fish were surveyed via seining in eight distinct habitats. We found that E. nuchale can use a greater diversity of habitats than previously appreciated, including both shallow and non-vegetated habitats. While densities of adult fish were higher in vegetated habitats, fish of all ages and sexes were found in non-vegetated habitats where structural diversity is provided by detritus or gravel. Males were most abundant in mats of aquatic moss, while females showed no strong habitat associations other than avoiding habitats with no shelter. Juveniles were mainly associated with aquatic moss and pools with detritus. The best conditions for in-stream vegetation favored by E. nuchale were in the spring pool where the channel was broad, the current slow and shallow margins were extensive. Our findings suggest that habitat conservation plans that reduce storm water runoff and increase streambed and riparian stability, specifically in habitats downstream of springs that house E. nuchale, could promote aquatic vegetation growth and structural diversity, thus expanding the species usable habitat.