Morphological variation can enable species to successfully survive and reproduce in distinct habitats. Water scorpion (Nepa cinerea Linnaeus, 1758) occurs in different aquatic habitats from lentic to lotic conditions. We examined the morphology of N. cinerea collected from a diverse array of habitat types (creeks, canals, ponds) in order to explore possible morphological adaptations to the habitat. We addressed the following specific questions: (i) is there any morphological differences between specimens collected from distinct habitats, and if so, (ii) is it possible to relate differences in morphology of the N. cinerea to characteristics of the habitat structure? Altogether 121 individuals (69 males and 52 females) were sampled from 17 sampling sites in the catchment area of Lake Balaton (Hungary). 54 body parameters were determined on all individuals. According to five habitat parameters (bottom quality, current velocity of the water, water depth, submerse plant density, shading) sampling sites were clustered into two distinct groups. Submerse plant density proved to be the most important discriminating factor between the two groups. The morphology of the N. cinerea (both males and females) sampled from the two contrasting habitat types were different. No relationship was found between geographical position of the habitat type and body morphology of N. cinerea. Leg morphology, especially claws on the third leg and some body shape parameters showed relationships with habitat characteristics. These morphological variations, which may be the result of phenotypic plasticity, could contribute to an opportunistic habitat choice of the species.