The objectives of BIOMAN are (1) to develop reliable and cost-effective indices for measuring overall biodiversity in the water column of shallow water bodies; (2) to develop mathematical tools that allow prediction of the effects of human impact on biodiversity in shallow waters, including the prediction of the response to restoration measures; (3) to compile a database on the current state of biodiversity in a representative sample of European shallow bodies, covering the classical food web (fish, zooplankton, phytoplankton) as well as the microbial loop (bacterioplankton and heterotrophic protists), and also covering genetic diversity of zooplankton and diversity as measured through the egg bank; and (4) to develop a reliable method to evaluate the success of restoration measures. In a large-scale field survey covering 96 shallow standing waters along a north-south gradient in Europe, we focus on organisms occurring in the water column, belonging to the microbial loop (bacteria, heterotrophic nanoflagellates, ciliates) and the classical food web (phytoplankton, zooplankton, fish). The ponds and lakes studied differ widely in the degree of human impact (relatively pristine and successfully restored habitats versus heavily impacted ones), degree of isolation, structural diversity, nutrient loading and size. We compare different measures of biodiversity in terms of the indices used (e.g. Hill numbers), the functional resolution (trophic level), the type of biodiversity measured (taxon diversity, genetic diversity within taxa) and the approach used for taxon delimitation (morphological or genetic criteria). In parallel with our field survey, we also measure diversity in the resting egg pool, allowing a comparison of biodiversity in the active populations (field survey) and in the resting egg bank for specific groups of organisms (e.g. zooplankton) and potentially providing an estimate of potential diversity. A comparative multivariate analysis incorporating the data on the different trophic levels and levels of diversity (taxon versus genetic diversity) as well as the data on resting egg banks is used to develop a cost-effective and reliable measure of overall biodiversity. The field survey provides data on the current state of biodiversity and characteristics of the target state of biodiversity in European shallow lakes. The data are incorporated into mathematical models and an expert system to predictthe response of lakes to specific impacts (e.g. restoration measures) in terms of biodiversity, given the starting conditions of the lake studied. To back up our survey results, we also explore the relation between biodiversities at different trophic levels (zooplankton and phytoplankton) experimentally, and validate our indices and mathematical tools using existing data sets on experimental lake manipulations.