Understanding the ecological impacts of large-scale hydraulic projects is critical for maintaining ecosystem health while meeting human water needs. It is, however, currently hindered by a lack of direct evidence on ecological impacts associated with this type of project particularly on water quality and fish communities. Here, we characterized patterns and variations of fish communities and water quality in five impounded lakes of the Chinese South-to-North Water Diversion Project (SNWDP), with the aim of better understanding potential ecological impacts of inter-basin water transfers. We found that 1) the impacts of water transfer on water quality in the impounded lakes was generally characterized by hydrological parameters (e.g. total suspended solids, turbidity, transparency, chlorophyll a, dissolved oxygen, conductivity and total hardness) in an upstream-downstream direction; 2) increased hydrological connectivity may have favored biological invasion (e.g. Tridentiger bifasciatus) and promoted a potential biotic homogenization among the impounded lakes: and 3) there was a pattern of decreased fish abundance and biomass from the upstream to downstream lakes with fish communities strongly driven by changing water quality patterns across the impounded lakes. These findings improve our understanding of ecological impacts of large-scale hydraulic projects and provide a significant basis for water agencies with similar water transfer systems to optimize their water transfer management in order to minimize ecological impacts. (C) 2020 Elsevier B.V. All rights reserved.