Little is known about the micro-evolutionary processes shaping within river population genetic structure of aquatic organisms characterized by high levels of homing and spawning site fidelity. Using a microsatellite panel, we observed complex and highly significant levels of intra-river population genetic substructure and Isolation by-Distance, in the Atlantic salmon stock of a large river system. Two evolutionary models have been considered explaining mechanisms promoting genetic sub-structuring in Atlantic salmon, the member-vagrant and meta-population models. We show that both models can be simultaneously used to explain patterns and levels of population structuring within the Foyle system. We show that anthropogenic factors have had a large influence on contemporary population structure observed. In an analytical development, we found that the frequently used estimator of genetic differentiation, FST, routinely underestimated genetic differentiation by a factor three to four compared to the equivalent statistic Jost¿s Dest (Jost 2008). These statistics also showed a near-perfect correlation. Despite ongoing discussions regarding the usefulness of ¿adjusted¿ FST statistics, we argue that these could be useful to identify and quantify qualitative differences between populations, which are important from management and conservation perspectives as an indicator of existence of biologically significant variation among tributary populations or a warning of critical environmental damage.