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The present review with focus on the last decade (2000–2010) aims to (i) collecting the major hypotheses explaining freshwater biodiversity patterns, (ii) identifying the main stressors affecting freshwater biodiversity, and (iii) revealing information gaps regarding ecosystem types, organism groups, spatial and temporal scales to highlight research needs to better propose sound conservation measures. The comparative analysis addresses six organism groups ranging from microorganisms to fish in basins, rivers, lakes, wetlands, ponds and groundwater. Short-term studies at ecoregion and catchment scale focusing on invertebrates, macrophytes and fish in Palaearctic and Nearctic regions dominated. The most frequent hypotheses tested were the landscape filter concept, the species–area relationship, the metacommunity concept. Dominating natural drivers were area, heterogeneity and disturbance. Land …