Freshwater lakes across the world have undergone dramatic changes in biological components and water quality over the past several decades. Previous studies focused on potential drivers mainly on nutrient enrichment in the catchment. However, the relative importance of climate change and the top-down cascade effects of fish stocking on water quality is not fully understood. Here, by compiling 155 lakes data with four periods of field investigation in subtropical lakes in China, we found no significant changes in water total nitrogen and total phosphorus in the past two decades. However, the phytoplankton abundance increased significantly, and the water clarity declined by 44.1%. We further found that carp stocking and climate change are potentially more important than nutrients driving water quality change, which is also evidenced in two lakes (Lake Donghu and Qiandao) with long-term monitoring histories. Specifically, carp stocking can decrease the water clarity directly by stirring up sediment and indirectly by trophic cascade along the food web. For climatic factors, mean annual temperature (MAT) has a positive effect on phytoplankton abundance, while mean annual precipitation has a negative one, with climates overall having little effect on water clarity. In addition, nutrient enrichment and climate change also have strong interactions with carp stocking, which may enhance the top-down effects on water quality. Our findings highlight that either MAT or carp stocking may become an overwhelming driver of water clarity decline, which provides new insights into the conservation strategy for water quality management in the subtropical lakes in China.The cluster of subtropical lakes in the Yangtze River floodplain is one of the largest groups of shallow lakes in East Asia (Wang and Dou 1998). These lakes are among the most threatened ecosystems in China due to long-term intense anthropogenic pressure and water quality degradation. More than 40% of lakes in this region were in a eutrophic state. Previous studies have assessed the long-term changes in water quality across the floodplain lakes indirectly by reconstructing paleolimnological records (Xu et al. 2017;Zhang et al. 2019) and remote sensing archives (Feng et al. 2019a,b;Hou et al. 2020). However, to date, direct long-term data from large-scale spatial investigation is scarce.Water clarity is a fundamental characteristic of lakes and provides general information on water quality. It reflects how