The Black Sea is a significant European watershed, more productive than the nearby Mediterranean, with dynamic wetland habitats along the shore and at the river mouths. Seasonal dynamics that sustain food webs that are adapted to the brackish, nutrient-rich environments are determined by the physiochemical conditions. River discharges carry phosphorus and nitrogen ions with high molar ratios into the Black Sea coasts. The present study evaluated the variations in water quality parameters between the winter season of 2020 and summer season of 2019 at 54 stations representing the two major rivers mounts (the Sakarya and Yeşilırmak), Samsun’s port and urban wastewater treatment outflow. Yeşilırmak River showed much higher nitrogen concentrations in the winter (̴ 1.46 µM) compared to the summer (̴ 0.10 µM). In addition, the Sakarya River nitrogen concentrations were similar between winter and summer seasons. The total phosphorus (̴ 2.25 µM) and chlorophyll-a (̴ 6.36 µg/L) concentrations were high at Samsun stations in the summer season 2019, where the pressure of urban wastewater is significant. The state of pollution, the sources of pollution, and their quantitative contributions in river basins and coastal regions must be determined for effective pollution control and water resource management.