The Meriç River is the longest river of the Balkans and it can be declared as most important aquatic ecosystem in the Thrace Region of Turkey. The Tunca and Ergene rivers are the most important branches of the Meriç and they are known to be exposed to important organic and inorganic pollution from agriculture and industry in their basins. We evaluated the sediment quality of the three rivers by determining a total of 25 trace and toxic element accumulations, including lithium (Li), boron (B), sodium (Na), magnesium (Mg), aluminum (Al), potassium (K), calcium (Ca), vanadium (V), chromium (Cr), manganese (Mn), iron (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn), gallium (Ga), arsenic (As), selenium (Se), strontium (Sr), silver (Ag), cadmium (Cd), antimony (Sb), barium (Ba), titanium (Ti), and lead (Pb). Also, oneway ANOVA testing was used to determine the statistical differences of element accumulations among the stations, and cluster analysis (CA) was used to classify the rivers according to sediment qualities and to classify the elements according to accumulation levels. As a result of the study, statistically significant differences were identified among the investigated rivers in terms of almost all the trace and toxic elements and the contamination levels of investigated aquatic ecosystems as follows: Ergene River > Meriç River > Tunca River in general. According to the results of elemental CA, five statistically significant clusters were formed: “most intense elements,” “second most intense elements,” “moderately intense elements,” “second rarest elements,” and “rarest elements.” According to the results of locational CA, two statistically significant clusters were formed: “highly contaminated locations” and “moderately contaminated locations.”