The spatial distribution of organisms is maintained by a combination of in situ reproduction and dispersal of conspecifics from elsewhere within its habitable range. The determination of dispersal origin and sub-population connectivity has a vital role to play in forming effective management policies. The common roach (Rutilus rutilus) is an important component of the economically and socially valuable recreational fishery and represents a well-studied member of the Cyprinidae. Microsatellite allele data were used to investigate hypothetically variant levels of microevolutionary structuring and isolation-by-distance (IBD) in in the Rivers Stour and Thames. A strong signal of IBD was found in the Stour, probably due to the limited capacity for unrestricted bidirectional dispersal in this river compared with the Thames. A weak inference of IBD in the Thames is likely erroneous and effected by a strong localised genetic signal from a recent stocking event. Whilst we found significantly genetically divergent upstream areas in the River Stour, a strong signal of IBD remained when the headwater sub-population was removed, suggesting that that the signal is not biased by non-equilibrium conditions in upstream reaches. We discuss these results with reference to the management of aquatic bioresources and emphasise the idiosyncrasy that aquatic biota and hydrological complexity may imprint upon patterns of biodiversity within any given system.