The Meriç River is the most important aquatic ecosystem in the Thrace Region of Turkey and the longest river of the Balkans. In the present study, water quality of the Meriç River in the rainy season was investigated and the pressure of the Tunca and Ergene rivers on the system was evaluated by a statistical approach using cluster analysis (CA). Water samples were collected from five stations (two of them from the downstream the Tuna and Ergene and three from the Meriç) in spring 2015. A total of 19 physical, chemical, and biological water quality parameters – including temperature, dissolved oxygen, percentage of oxygen saturation, pH, conductivity, TDS, salinity, turbidity, nitrate, nitrite, ammonium, phosphate, sulfate, chemical oxygen demand, biological oxygen demand, total carbon, total inorganic carbon, total organic carbon, and cyanide – were measured. According to detected data, pollution levels of the investigated rivers were as follows; Ergene River > Tunca > Meriç River. It was also determined that the Ergene and Tunca reduce the water quality of the Meriç significantly after they fall. And also according to the results of CA, three statistically significant clusters were formed, which corresponded to the Ergene (Cluster 1); upstream and midstream of the Meriç (Cluster 2), and downstream of the Meriç and Tunca (Cluster 3).