Sympatric fish populations observed in many north temperate lakes are among the best models to study the processes of population divergence and adaptive radiation. Despite considerable research on such systems, little is known about the associations between ecological conditions and the extent of ecotypic divergence. In this study, we examined the biotic and abiotic properties of postglacial lakes in which lake whitefish, Coregonus clupeaformis, occur as a derived dwarf ecotype in sympatry with an ancestral normal ecotype. We compared 19 limnological variables between two groups of lakes known from previous studies to harbour sympatric dwarf and normal ecotypes with high and low levels of phenotypic and genetic differentiation respectively. We found clear environmental differences between the two lake groups. Namely, oxygen was the most discriminant variable, where lakes harbouring the most divergent populations were characterized by the greatest hypolimnetic oxygen depletion. These lakes also had lower zooplankton densities and a narrower distribution of zooplantonic prey length. These results suggest that the highest differentiation between sympatric ecotypes occurs in lakes with reduced habitat and prey availability that could increase competition for resources. This in turns supports the hypothesis that parallelism in the extent of phenotypic divergence among sympatric whitefish ecotypes is associated with parallelism in adaptive landscape in terms of differences in limnological characteristics, as well as availability and structure of the zooplanktonic community.