Waters provide essential needs both for human societies as well as natural ecosystems. Floating solar PV (FPV) applications on water bodies are currently in strong demand worldwide. Floating solar PV system is a new concept in renewable energy with the solar plants by harnessing available water surface, such in dams, lakes, and other water bodies. Although the floating solar PV industry is becoming more and more popular, the study on the biological, chemical, and physical properties effects of using FPV cover on natural water coverage—especially in tropical countries—has not been widely carried out yet. This paper aimed to evaluate the effect of floating solar PV on temperature, DO (dissolved oxygen), TDS (total dissolved solids), total phosphorus concentration, and chlorophyll-a concentration using mesocosm experiments to understand the biological, chemical, and physical process under closed environment. The experiment was conducted in a natural water body, Mahoni Lake, in which a total amount of 7 water samples were collected from each mesocosms. The results show that the floating solar PV reduces the average temperature, DO, conductivity, TDS, and chlorophyll-a concentration changes (p-value < 0,05); and the floating solar PV does not directly reduce the average total phosphorus concentration due to high probability of thermal stratification (p-value > 0,05).