Due to the extreme differences in environmental factors between subterranean and surface environments, subterranean habitats and animals therein are an excellent model system for studying ecological speciation, i.e. the origin of new species as side effect of divergent natural selection. The freshwater isopod crustacean waterlouse, Asellus aquaticus, has colonised the underground several times independently and has still living surface populations. There is practically no gene flow between surface and subterranean populations, suggesting a reproductive isolation must exist among them. In two surface-subterranean population pairs of waterlice (Planina Polje-Pivka River in Planina Cave, Cerknica Polje-Rak River in Planina Cave), we measured the ability of individuals to resist water current and checked if this trait could act as a reproductive barrier. Critical water current velocity (i.e. the velocity of water current at which waterlouse was washed away) was measured for 160 individuals, 20 males and 20 females from each population. The subterranean waterlice from Pivka River resisted a faster water current than the surface waterlice from Planina Polje, but no difference in the critical water current velocity was found between the subterranean waterlice from Rak River and the surface waterlice from Cerknica Polje. Individuals of both subterranean populations also had a higher predictability of the critical water current velocity compared to surface individuals. We assume that differences between both subterranean populations may be a consequence of different hydrology of Pivka and Rak River in Planina Cave. The differences between ecomorphs are probably too small to function as a reproductive barrier. To determine whether the measured differences are crucial for keeping the subterranean waterlice in the underground and washing out the surface waterlice, water current velocity should be measured in the natural habitat of these populations.