<p>In plants, dependence on clonal reproduction via rhizomes or other vegetative means has a significant influence on population genetic structure. This is further complicated in aquatic systems in which hydrochory may play a role in dispersal both within and among populations. Data suggests that in these instances, upstream populations may be genetically eroded as downstream populations become more genetically diverse. In the present study, we test this hypothesis in the case of an endangered emergent aquatic plant (<i>Sagittaria fasciculata</i>; Alismataceae) that is thought to be dependent on clonality and hydrochory. We developed 35 nuclear microsatellite loci for genotype-by-sequencing of 282 individuals across 15 colonies spanning the species range. All ramets were mapped and clonal assignment was overlaid to determine extent and distribution of clones. Our results indicate that <i>S. fasciculata</i> is highly dependent on clonal reproduction, with three sites exhibiting only a single multi-locus genotype or clone. The greatest genetic variation was observed among three sites occurring in close proximity (&lt; 100&#xa0;m), and here we observed evidence of low genetic diversity upstream relative to downstream, supporting the hypothesis of unidirectional gene flow as a result of hydrochory. In the context of species recovery, our data reiterate that stem counts are not an appropriate metric to assess population size or vigor. Additionally, the combined impacts of clonal reproduction and hydrochory of propagules means that greater attention should be given to recovery of colonies within relatively close proximity to each other to support the development of a robust and genetically diverse population.</p>