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There are over 300 lakes interconnected by riverbranches and man‐made canals in the Danube Delta (Romania). A multidisciplinary survey of these riverine lakes situated in large wetland complexes was made comprising hydrological modelling, remote sensing and monitoring of water quality, plankton, aquatic vegetation and fish communities. Between‐lake differences in water quality and aquatic vegetation cover were inferred from satellite image. Based on channel and lake dimensions, hydrological characteristics of the lakes in the delta were determined: hydrological distance from a riverbranch, residence time and impact of reed water. Water‐quality and biotic parameters (phyto‐ and zooplankton, submerged plants and fish) were sampled in a comparative survey in June 1997–1999 in subsets of the lakes. In a follow‐up study in 2001–2002, seasonality of aquatic vegetation and fish were recorded.