Rotifer structure may serve as predictor of environmental features, including temperate subclimates between water bodies. The difference in latitude between two temperate regions (Poland vs. Croatia) affects the identification of particular environmental factors that subsequently influence the taxon-related indices of rotifers. A study on 10 water bodies found that taxon-trait indices were sensitive in identifying latitude differences, even though extreme weather conditions were not considered, and only two seasons (spring and autumn) were examined. A variable rotifer community, with a high share of rare species, was obtained. We found a distinctiveness of abiotic factors between both countries, indicating a higher trophic state in Poland. Although habitat conditions were more similar in spring compared to the autumn, the percentage of rotifer common taxa was alike in both seasons but variation in distinct species community was clear. Trophic state increase in Poland was reflected in the structure of dominant and distinct species, with a wide range of eutrophy indicators. Comparing how rotifer species respond to environmental conditions is important for developing methods to assess trophic state changes due to climate change. Single species, distinct or rare species, are often the first sign of changes.