Nutrient-rich freshwater ecosystems are generally considered as having low ecological quality and low associated biodiversity. In such systems we analysed the effects of water quality on biodiversity of several species groups, to determine tipping points and tools for monitoring. We investigated the water quality of 99 eutrophic and hypertrophic shallow lakes with extensive fish culture during a 3-year study, through the measures of physico-chemical parameters, phytoplankton biomass and structure. In a second step, we related the water quality with richness of aquatic plants, macroinvertebrates and dragonflies. With concentrations of chlorophyll-a above 30 or 70 mu g l(-1), shallow lakes are normally classified, respectively, in a poor or bad ecological state. However, our results show that chlorophyll-a concentrations up to 78 mu g l(-1) could be found together with relatively high species or family richness of aquatic plants, invertebrates and dragonflies. We identified most tipping points with 50-60 mu g l(-1) of chlorophyll-a, values above which a significant decrease of species diversity was found. For monitoring of these shallow lakes we propose to use chlorophyll-a concentrations in combination with water transparency during spring. These parameters are easily applicable and cheap and they yield a good forecast of the biodiversity for the species groups studied.