Understanding populations’ genetic connectivity is critical for conservation and management measures. Most population connectivity studies conducted in aquatic plants have been centered on linearly arranged systems wherein a cline in genetic diversity is expected to the downstream. However, non-linear systems and lakes characterized by hydrological mixing, circulation, and strong discharge might not support this assumption. Considering these processes and the mixed reproductive mechanisms of Cyperus papyrus (L.), we assessed the relative role of hydrological connectivity and vegetative dispersal in shaping the clonal and genetic structure of the species. Four hundred and two papyrus individuals from 13 populations fringing Lake Tana, Ethiopia, were genotyped using 15 microsatellite markers. Despite the genetic bottleneck detected, papyrus populations maintained moderate levels of clonal (R = 0.48) and genetic diversity (HE = 0.40). We found a significant withinlake level of genetic differentiation (F0 ST = 0.16; DEST = 0.10). Bayesian analysis assigned individuals to three non-panmictic genetic clusters. Evidences of long-distance vegetative dispersal and asymmetrical contemporary migration were detected among C. papyrus populations. The patterns of the genetic structure, clonal dispersal, and migration rate partly correspond to the surface flow. Overall, hydrological connectivity and vegetative dispersal shape the clonal and genetic structure as well as the connectivity of C. papyrus populations in Lake Tana.