Many studies emphasized the role that water mites play within the invertebrate communities of spring ecosystems, regarding species diversity and its significance within the crenal food web, as well as the specific preferences water mites exhibit towards spring typology. In pristine natural springs with permanent flow, water mites are nearly always present and usually display high diversity. This study aimed to determine whether significant differences in water mite assemblages between rheocrene (river-forming springs with dominant riffle habitats) and limnocrene (lake-forming springs with dominant pool habitats) karst springs could be detected in terms of species richness, diversity and abundance, but also in different ratios of specific synecological groups: crenobiont (exclusively found in springs), crenophilous (associated with springs) and stygophilous (associated with groundwater) water mite taxa. Our research was carried out on four limnocrenes and four rheocrenes in the Dinaric karst region of Croatia. Seasonal samples (20 sub-samples per sampling) were taken at each spring with a 200-µm net, taking into consideration all microhabitat types with coverage of at least 5%. Water mite abundance was found not to differ between morphological spring types. Significantly higher values of species richness and diversity indices were found in rheocrenes compared to limnocrenes, like those usually reported for this type of springs. However, unlike the studies previously reported, in this case, the higher shares of crenophilous and crenobiont water mite individuals were found in limnocrenes. The differences between stygophilous water mite taxa ratios among spring morphotypes were not statistically significant, indicating that the degree of the groundwater/surface water interaction (and water mite interaction therein) does not seem to be directly influenced by spring morphotype. Within this research, 40% of identified water mite species (eight out of twenty) were recorded for the first time in Croatia, thus highlighting again a huge gap in water mite knowledge of karst springs.