It is increasingly recognized that populations of marine organisms with potential for large-scale dispersal may exhibit fine-scale genetic structure. The Gulf of Gdañsk (Poland) is an interesting setting to study fine-grained population structure in marine organisms as it is characterized by chronic anthropogenic pollution and strong salinity gradients. We investigated, at two nested spatial scales (35 and 7 km), genetic structure among populations of the infaunal tellinid bivalve Macoma balthica. The COI mitochondrial marker revealed a likely mix of evolutionary lineages in the Gulf, with no detectable spatial structure. Seven microsatellite markers detected weak population structure, separating deep and shallow populations within short distances (7 km) and assignment tests suggested asymmetric gene flow among these populations, with no shallow recruits being detected in deep waters. Given the specific environmental conditions encountered at deeper depths in the Gulf (increased salinity, lower temperatures, oxygen depletion, hydrogen sulfide pollution), we suggest that deeper populations may be subjected to local adaptation.