Earlier studies of habitat-specific subpopulations of mixed clonal and sexual freshwater snails of the species Potamopyrgus antipodarum have revealed clinal variation by depth in several life-history traits, risk of parasite infection, mixed population structure, and the genetic structure of the clonal population. Clinal variation is pronounced in life-history traits: snails are larger and start reproduction later in the deeper habitats. The proportion of clonal individuals increases with depth, and many clones are habitat-specific. While these patterns are well documented, it is not known which processes have led to the observed genetic divergence in the clonal population. In this study, we experimentally investigated the contribution of phenotypic plasticity to habitat-specific life-history trait variation using reciprocal transplant experiments with adult and juvenile snails. Assessment of phenotypic plasticity is important because canalized habitat-specific life-history trait variation is one of the alternative explanations for habitat-specific genetic divergence seen in the clonal population. However, if life-history trait variation is largely due to adaptive phenotypic plasticity, canalized optimization of life-history traits is unlikely to explain the divergence observed in the clonal structure. We found significant habitat-induced variation fur growth rate, proportion of brooding females, brood size, number of surviving offspring, and juvenile survival, indicating that much of the life-history variation must be considered the result of phenotypic plasticity. Based on these results, it seems that life-history trait divergence is unlikely to explain habitat-specific clonal structure. In contrast, we found genetically based differences in resistance to parasite infections, snails of the deeper Isoetes habitat were more susceptible to infection than snails of the shallow shorebank habitat. To our surprise, we found only a few habitat-by-origin interactions that could directly contribute to the maintenance of the observed habitat-specific clonal structure. One potentially important interaction, however, was that in the deeper Isoetes habitat, reproductive output of snails transplanted from the shallow habitat was lower than that of resident snails. In addition, we also found that survival of clonal snails may be poorer in unfamiliar habitat's than that of sexual P. antipodarum, potentially promoting the maintenance of habitat-specific clonal assemblages. Thus, higher parasite resistance of shallow-water snails in both habitats and lower reproductive output of shallow-water snails in the deep habitat are likely to contribute to the maintenance of the habitat-specific clonal structure in P. antipodarum populations, whereas most of the observed variation in life-history traits seems to be due to phenotypic plasticity, which is likely to be adaptive.