The Meriç River, the longest river of the Balkans, is the most important aquatic ecosystem within the Thrace Region of Turkey, along with its main tributaries, the Tunca and Ergene Rivers. In this study, the sediment quality of Meriç, Tunca, and Ergene Rivers was evaluated by using the Potential Ecological Risk Index (RI) and the Biological Risk Index (mERM-Q), both widely used methods in sediment quality assessment studies, to assess the ecological and biological risks of heavy metals within the river ecosystems. According to the results of the Biological Risk Index, nickel and chromium displayed the highest risk factors, and in terms of the Potential Ecological Risk Index, cadmium yielded the highest risk factor across all the investigated lotic ecosystems.