In this study, the authors aimed to compare the performance of the physicochemical-based water quality metrics (WQI, SWQMR) and diatom-based diatom metrics (TDI, BDI, GDI) to evaluate the water quality and ecological status of the Mert Stream. A total of 104 epilithic diatom species, belonging to 44 genera, were recorded during the study period. Navicula was the most dominant diatom in the sites near intensive farming areas, while Gomphonema was the most dominant species in the sites in vicinity of urban and industrial settlements. According to the water quality indices based on the physicochemical parameters and diatoms, the water quality in the upper and middle parts of the Mert stream was better than in the lower parts (higher amount of total suspended solids and higher conductivity). The structure of the epilithic diatom community was mostly shaped by total suspended solids, electrical conductivity and nutrients according to Canonical Correspondence Analysis results. The obtained results revealed that diatom metrics, especially GDI, and water quality metrics, especially WQI, can be used for the monitoring of lotic systems and provide useful complementary information on the ecological status of rivers in medium rainfall regions such as Samsun.