Résumé
Habitat modification by humans has severe impacts on the biotic and abiotic components of freshwater ecosystems. In China, shallow lakes in the Yangtze River basin are facing major habitat modification owing to the loss of their natural connections with rivers and the development of aquaculture. In this study, temporal data (ranging from 1970 to 2010) from a set of lakes (n = 8) were used to quantify the abiotic and biotic consequences (i.e. taxonomic and functional diversity of fish communities) of such human activities. There were significant abiotic changes that mainly occurred after the 1990s. Specifically, water transparency decreased and the total nitrogen content of the lakes increased considerably. A trend (although not significant) was detected towards a decrease in fish species richness over the period studied. The taxonomic dissimilarity (i.e. beta‐diversity) among fish communities decreased significantly over the years, indicating a strong homogenization of the fauna across the lakes. In addition, it was found that fish functional diversity has decreased in most lakes since the 1970s. In particular most migratory fish species with long life‐spans and large body size disappeared from the lakes, hence contributing substantially to the observed decrease in functional diversity. Based on the findings, it is argued that both the abiotic and biotic integrity of the lakes were seriously affected after the lakes lost their connections to the rivers. It would therefore be helpful to reconnect the lakes to rivers with wise sluice‐gate management, and regulate fishery activities in those lakes to restore fish diversity.