This study was intended in paddy (rice husk and rice), sediment, and irrigation water samples taken from the paddy fields of Ergene River, Meriç River, and Yenikarpuzlu Dam reservoir which are frequently grown in the river basin in Thrace region and endosulfan (EN) and PAHs were investigated. For analysis, EN and PAHs were studied by GC-MS. The data obtained as a result of the analyses were compared with the results of the standard reference items, and the accuracy of the results was determined. The standard addition method was used to prove the accuracy of EN and PAHs. The recovery parameters on the extraction efficiency of EN and PAHs were optimized, and the recoveries ranged from 82 to 105%. The methods showed good linearity for EN and PAHs, and the LOD and LOQ for methods were found 0.03–63.1 and 0.1–210 μg kg−1, respectively.