Many ecological assemblages show a nested subset pattern of species distribution, i.e., common species occur in all assemblages, whereas rare species tend to occur in progressively more diverse assemblages. We examined the determinants of nestedness and assemblage composition of lake-dwelling snails and clams in a boreal landscape using nestedness calculator, rank correlation, and canonical correspondence analysis (CCA). Both snail and clam assemblages were highly nested, and the nested subset pattern correlated with an index of isolation and habitat suitability (mainly water chemistry) for snails and with habitat suitability for clams. Habitat suitability and isolation were themselves highly correlated, thus obscuring the detection of their relative importance to nestedness. Yet, it appears that nestedness in this molluscan fauna is due mainly to nested tolerance of abiotic factors. Partial CCA showed that isolation and habitat suitability were almost equally important correlates of species composition for snails, whereas lake area was the key factor related to clam assemblage composition, followed by habitat suitability. It thus appears that while the degree of nestedness in species composition of lake-dwelling clams and snails may be highly correlated with a single variable, the overall pattern of species composition among lakes requires multiple explanatory variables.