Springs are often recognized as biodiversity hotspots on the regional scale but at the same time they are among the most endangered freshwater habitats. Water mites are among the aquatic animal groups with highest share of crenobiotic (=spring-dwelling) species and, therefore, are possibly the best indicators of the ecological status of spring habitats. We studied water mites and environmental factors correlated with their distribution pattern along a eucrenon-hypocrenon gradient. The sampling was conducted in 14 karstic springs located in the Mediterranean part of Montenegro. We collected 17 water mite species of which four species were crenobiotic. We did not find significant differences between the water mite assemblages from the source and springbrook. Similarly, there were no significant differences in number of species and abundance between the studied spring sections, neither for crenobiotic taxa nor for non-crenobiotic taxa. We found that the number of non-crenobiotic taxa was predicted mainly by water depth, whereas the abundance of crenobionts was most strongly associated with temperature. No significant predictors for the number of crenobiotic species in spring habitats were found. Our results revealed also that distance from the nearby water body was the main driver of the crenobiotic species abundance in eucrenon suggesting the large effects of the local flooding events on crenobiotic species. Water mites may help in assessing the response of crenobiotic assemblages in those spring habitats which likely to be flooded in future as the results of ongoing climatic changes.