Current methods for assessing lake trophic status using zooplankton are well-established, but there is a lack of approaches for small, shallow water bodies. This study addresses the gap by analyzing rotifer communities across 100 ponds in different catchment areas (field and forest). We hypothesized that the Rotifer Trophic State Index (TSIROT) is an effective tool for assessing trophic state, yielding comparable results to the Carlson TSI index. We also proposed that variations in physical and chemical parameters would significantly affect rotifer composition, impacting the trophic state assessment. Field ponds, exposed to agricultural runoff, exhibited higher trophic states and a predominance of detritivorous species. In contrast, forest ponds, with extensive macrophyte coverage, maintained lower trophic states and supported diverse algivorous species, particularly of littoral and mesotrophic origin. This confirmed our hypothesis that catchment type strongly influences trophic state and rotifer communities. We demonstrated that rotifer traits—abundance, species diversity, habitat type preferences and proportions of eutrophic versus mesotrophic species—along with TSIROT, are effective in assessing water quality in ponds. Overall, the results validate TSIROT as a reliable tool for small water bodies, comparable to Carlson’s TSI index, and highlight the importance of catchment type in influencing water quality.