Lake Koca (Dalaman), a wetland in the western Mediterranean basin of Türkiye, is an extraordinary lake with salty, fresh, and sulfurous waters and is home to high biodiversity. The present study examines the spatial and seasonal variation in fish communities and assesses the influence of environmental parameters on the community structure of Lake Koca. A total of 1.530 specimens were captured, representing seven families and 11 species (2 non-native, 1 introduced, and 8 native species). Total fish abundance and richness were higher at the littoral than at the limnetic zone, but no seasonal variation was observed. Non-native fish species, Coptodon zillii, was the most abundant in the littoral zone, followed by species of Mugilidae. The abundance of the two endemic fish species (Capoeta aydinensis and Ladigesocypris irideus) was relatively low in both habitats. Shannon-Wiener diversity index and evenness did not vary seasonally and spatially. Fish abundance and richness were significantly and positively correlated with chlorophyll-a and macrophyte coverage while negatively correlated with depth. Spearmen’s Correlation analysis revealed that native fish species show a relationship with the chemical parameters of the water, while C. zillii showed a distribution related to depth and macrophyte density. Both anthropogenic activities and the presence of non-native fish may affect the distribution and abundance of endemic fishes.