The Meriç River is located in the Thrace Region of Turkey, which has great importance in terms of agricultural potential and is known as “Rice Land”. The Meriç is also the longest river in the Balkans and is known to be exposed to intensive pollution by means of special agricultural pressure on the system. The aim of this study was to determine pesticide accumulation in water and sediment of the Meriç River Basin. For this purpose, water and sediment samples were collected in spring (rainy) of 2017 from 24 stations selected on the basin and pesticide contents. A total of 174 different pesticide varieties were investigated in water and sediment samples using liquid chromatograph mass spectrometry LC/MS. According to detected data, the concentration of pesticide residues ranged from 30.4 ng/L (thiabendazole in Meriç River) to 291,310 ng/L (carbendazim in Ergene River) for water samples, and from 12.4 ng/L (spiroxamine in Gala Leke) to 15,947 (carbendazim in Ergene River) for sediment samples. There was a clear dominance of the carbendazim in all the investigated aquatic habitats. It was also determined that pesticide concentrations detected in the Meriç River Basin, especially in the Ergene River, were found to be at quite high levels and the system has Class III–IV water quality in terms of total pesticide accumulation.