Along with the increasing demand for energy and pressure to reduce carbon emissions, floating photovoltaic (FPV) systems are increasingly built on the surface of water bodies with the aim to produce clean energy. However, little is known about how FPV systems influence freshwater ecosystems, e.g., their zooplankton communities. We investigated how rotifer communities responded to FPV systems in subsidence wetlands created by underground coal mining in the North China Plain. Diversity metrics of the rotifer communities were compared between wetlands with and without FPV systems. The density of rotifers was higher in wetlands without FPV systems. In contrast, rotifer diversity as represented by Shannon-Weiner and Pielou evenness indices was higher in the FPV-covered wetlands, while there was no difference in species richness between the two types of wetlands. Furthermore, community structures differed between the two types of wetlands, in large part reflecting differences in the relative abundance of five dominant species found in both types of wetlands. These differences in rotifer assemblages were in large part explainable from environmental changes caused by the FPV panels, notably reduced light availability and water temperature, leading to reduced phytoplankton production. These findings show that FPV systems cause major changes to rotifer communities in these subsidence wetlands and likely in wetlands more generally, and monitoring of the longer-term effects is recommended given the fundamental role of zooplankton in freshwater ecosystems.