Harperella (Ptilimnium nodosum) is a federally endangered plant species with a large population along Sideling Hill Creek, Allegany and Washington Counties, Maryland. Monitoring of this species is difficult owing to the unpredictable flood events that change the distribution and composition of stream substrates of its rocky shoal habitat. We characterized substrate types in 80 quadrats using two methods of nonmetric multidimensional scaling (NMS and MDS). We employed multiple-response permutation procedure (MRPP) to examine differences in substrate composition between habitats occupied (N  =  52) and unoccupied (N  =  28) by Harperella. The NMS and MDS ordinations show that Harperella cover and amount of fine sediments are positively associated. Harperella occupies specific microhabitat with high cover of fine sediments, often held in crevices of exposed bedrock. The MRPP results demonstrated that substrate composition in occupied versus unoccupied habitats differ significantly. This difference is chiefly attributable to cover of fine sediments in occupied habitats and cobble, gravel, and sand in unoccupied habitats. We conclude that the local distribution and abundance of Harperella patches in Sideling Hill Creek is constrained by the abundance of appropriate substrate microhabitat in any given year and recommend that annual census be modified to focus on large persistent patches.