Riparian landscapes are dynamic systems and exhibit considerable spatio-temporal variation in stream flow and physical composition of stream substrates that provide habitats for many species. We investigated genetic diversity and population genetic structure of Harperella nodosa (Harperalla; Apiaceae), a federally endangered semi-aquatic plant. We employed a unique study design that involved sampling at regional, stream, and fine scales in 3 riverine systems in Maryland and West Virginia. Using intersimple sequence repeats (ISSRs), we found high levels of genetic diversity at all scales and pronounced fine-scale genetic structure. Pairwise correlation between geographic and genetic distance was scale-dependent. This study illustrates that temporal monitoring and multiple-scale plans are essential for conservation management programs for Harperella.