Warna and Pengilon Lakes are very close to each other and connected with the sill, a famous tourist destination in the Dieng Plateau Java. Land-use changes are the main problem that affected the lakes. The conversion of forest into an agricultural area had induced erosion and increased the volume of nutrients discharged to the lake due to high use of fertilisers in potatoes farms. In the dry seasons, water from those lakes was pumped to irrigate agricultural land. This study aimed to determine the water quality of Warna and Pengilon Lakes based on physical, chemical parameters, and phytoplankton communities. Water samples were collected from 4 sites at each lake to analyse biological oxygen demand (BOD), chemical oxygen demand (COD), ammonia, nitrate, nitrite, and total nitrogen (TN). Temperature, pH, dissolved oxygen (DO), turbidity, and conductivity (EC) were measured in-situ. During this research, turbidity and BOD in Warna and Pengilon Lakes exceeded the Indonesian water quality standard. Based on the STORET method, the water quality of Lake Warna was assessed as highly polluted for all classes. However, based on the pollution index (PI), Lake Warna was slightly to moderately polluted, as well as the saprobic index was in the β-mesosaprobic phase. Based on the species diversity index of phytoplankton, both Warna and Pengilon Lakes were moderately polluted. The long-term monitoring studies are necessary as an early warning sign of water quality degradation. Therefore, they provide insight into the overall ecological condition of the lake and can be used as a basis for developing suitable lake management.