In order to determine whether using indicators of zooplankton diversity and macrophyte parameters (density and biomass) could be a useful tool for diagnosing the water quality of ponds we hypothesised that in various trophic types of shallow water bodies parameters of a macrophyte habitat will reflect zooplankton diversity. Thus, 439 stations (open water, helophytes, elodeids) were studied among 274 pastoral ponds (mid-west Poland). In each trophic state of waters a key predictor of zooplankton diversity was biomass of macrophytes attributed to a variety of ecological types or various species of macrophytes. A shift from the high importance of elodeids (e.g. Myriophyllum, Ceratophyllum demersum) in structuring zooplankton diversity in mesotrophic waters to helophytes (Typha angustifolia, Phragmites australis, Schoenoplectus lacustris) in hypereutrophic ponds was recorded. Hypereutrophy proved to be extremely unfavourable for zooplankton, as reflected in its lowest diversity; rotifers reached their optimum in eutrophy and crustaceans in mesotrophy. Adverse environmental conditions in hypereutrophic waters caused the elimination of macrophyte-dominated refuges, thereby lowering the macrophyte-site share, which ranged from 47% in eutrophy, 40% in mesotrophy to only 20% in hypereutrophy. Therefore, we assume that zooplankton diversity and macrophyte occurrence can be used for quality assessment of small water bodies.