Large zooplankton can efficiently graze on algae and thereby improve water quality. However, zooplankton body size is considered to decrease with decreasing latitude because of the high fish predation and warm temperatures at lower latitudes. To explore how fish stocking has destabilized the trophic cascade and influenced water quality along a latitudinal gradient of reservoirs, we compared zooplankton body size and trophic cascades to water quality indicators in the subtropical Lake Qiandaohu and in tropical Guangdong reservoirs. The results showed that the body length and total biomass of the dominant zooplankton in Lake Qiandaohu were much larger than those of zooplankton in the Guangdong reservoirs. Moreover, fish predation was the key factor influencing the changes in zooplankton body size and total biomass in Lake Qiandaohu. In the Guangdong reservoirs, water temperature and total phosphorus were the pivotal drivers of zooplankton body size and biomass, respectively. In addition, structural equation models showed that the decreasing zooplankton body size and biomass under fish pressure weakened the grazing pressure on phytoplankton and indirectly contributed to the low water clarity in Lake Qiandaohu. However, fish had little influence on the inefficient algal grazing of zooplankton in the Guangdong reservoirs. Overall, zooplankton can function as an indicator of water quality in fish-controlled subtropical reservoirs but not in nutrient-controlled tropical reservoirs.