The evaluation of water quality is commonly conducted by measuring physicochemical parameters. However, to enable identification of water quality changes of aquatic ecosystems, such as lakes, requires long time series data sampling. In this study, we performed water quality assessments by utilising the presence of potential harmful algae presence in Lake Ranu Grati, Indonesia. We conducted water sampling to evaluate 13 water quality parameters (in-situ and ex-situ) and identified the phytoplankton community structure of the lake at seven sampling sites from December 2018 to February 2019. To assess the water quality of the lake, we used two approaches. First, calculated the classical water quality index using the STORET method. Second, identified the potential harmful algae from the phytoplankton community structure of Lake Ranu Grati, and then determined the water quality factors related to its occurrence using canonical correspondence analysis. The results showed that water quality condition of Lake Ranu Grati was optimum except for COD, BOD and ammonia. The STORET index also classified the seven sites in Lake Ranu Grati as lightly polluted and moderately polluted. Considering the presence of potentially harmful algae from the Cyanophyta and Euglenophyta divisions, it was suggested that Sites 6 and 7 were the most polluted areas of Lake Ranu Grati, which corresponded to the high concentration of COD and BOD. This finding indicates that agricultural and aquaculture activities around the lake need to be controlled to maintain the sustainability of the water quality condition of Lake Ranu Grati.