Interspecific interactions between surface and subterranean species may be a key determinant for species distributions. Until now, the existence of competition (including predation) between these groups has not been tested. To assess the coexistence and potential role of interspecific interactions between surface Gammarus fossarum and subterranean Niphargus timavi, and to determine their micro distributions, we conducted a series of field and laboratory observations. We aimed to determine: (1) species substrate preference, (2) whether the presence of G. fossarum influences the habitat choice of N. timavi, and (3) possible predation effects on micro habitat choice of small juveniles. Throughout a small river in SW Slovenia, N. timavi was predominantly found in leaf litter and gravel, but rarely in sand. In the sand however, we exclusively found juveniles. In contrast, surface G. fossarum sheltered mainly in leaf litter. A similar, body size dependent, micro distribution was observed in G. fossarum, where small individuals were generally found in gravel and sand. The presence of G. fossarum affected the micro distribution of juvenile, but not adult, N. timavi. In the laboratory we observed predation and cannibalism in both species. Niphargus timavi, however, appeared to be a more efficient predator than G. fossarum. In particular, juvenile N. timavi were most vulnerable to preying by adults of both species. This probably affected the distribution of juvenile N. timavi that chose finer substrates when placed with adult individuals in an aquarium with granules of different size. To understand the distribution of subterranean species, the summed effect of intraspecific interactions, as well as surface – subterranean species interactions, in particular between individuals of different size, should be taken into account.