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. A clear distinction was found in three lake types: (1) inflow lakes at short distance to the river, with a high flushing rate, high load of suspended minerals but low chlorophyll concentrations, high cover of floating and submerged vegetation and dominance of eurytopic fish; (2) large, relatively deep lakes with moderately long residence time, high Potamogeton-cover that collapses during summer, and dominated by eurytopic fish; (3) smaller, isolated lakes at the longest distance from the river, with long residence time, of which the water quality is strongly influenced by water flows through large floating reedbeds ('blackwater'), with a high vegetation cover of Ceratophyllum demersum and Nitellopsis obtusa throughout the summer and a limnophilic fish community tolerant for low oxygen conditions. Aquatic vegetation showed a clear seasonality related to the interaction between plant development and light conditions. Seasonal changes in fish distribution within the system merely followed the vegetation trends in different lakes and the conditions in the river channels. Past trends in the trophic gradient are discussed in the context of hydromorphological modifications in the Delta. There is a high potential for restoring natural processes owing to the high connectivity and large scale of the system. Copyright (C) 2008 John Wiley & Sons, Ltd.