Phytoplankton groups are one of the major quality element to be used in the evaluation of the trophic and ecological state of freshwater ecosystems according to the EU Water Framework Directive. This research was made to assess the trophic and ecological status of Lake Bafa in Turkey, on the basis of phytoplankton communities. Büyük Menderes River is one of the most important factor that carries pollutants to Lake Bafa. The eight sampling station were assigned to evaluate the ecological and trophic state of the lake. Phytoplankton species were collected monthly for 2 years study period. Most commonly used phtoplankton indices Q index and Carlson’s Trophic State Index (TSI), and different versions of diversity indices were used to estimate trophic and ecological state of the lake. Similarities between the sampling stations were clustured by using the unweighted pair group method using arithmetic average (UPGMA), based on phytoplankton communities. Correlations between the applied indices were determined by using Pearson Correlation. After the identification of collected phytoplanktons, total of 63 taxa which belong to classis of Cyanophyceae (11.2%), Bacillariophyceae (49.2%), Chlorophyceae (23.8%), Xanthophyceae (1.5%), Euglenophyceae (11.2%) and Dinophyceae (3.1%) were detected. The 1st and 2nd stations were the most similar stations to each other (88%) according to phytoplankton communities. Secchi disc depth (SD) and TP played an important role in the distribution of phytoplankton species in Lake Bafa. The highest significant positive correlation was determined between Q and TSI (r = 0.987, p˂0.01). Considering the TDI values in the phytoplankton composition of the lake, it can be said that although the productivity status of the studied lake is still “mesotrophic”, it has a tendency towards “eutrophic” state. According to the Q values, the first five stations reflect the moderate ecological state, while the 6th, 7th and 8th stations represent the poor ecological state.