According to the water framework directive (WFD), the chemical status should be determined for each water body in a basin through monitoring and evaluation studies, and the gap between the status of water bodies and good water status should be revealed in river basin management plans. In this context, the methodology starting with the evaluation of the monitoring results of the priority substances (PSs) until the end of determining the measures to achieve good condition in surface waters was given in this study. The key aim was to provide a useful methodology defined as a matrix for determining the sources of pollutants that caused this gap. This matrix was applied to the most polluted sub-basin of Kucuk Menderes Basin located on the western part of the Turkey. Monitoring studies were carried out in 21 water bodies for a 1-year period for 45 PSs and monitoring results were compared with environmental quality standards (EQS). It was determined that 13 of 45 PSs in 15 water bodies exceeded the EQS. The common PSs in the basin were lead, nickel, fluoranthene, benzo(a)pyrene, C10-13 chloroalkanes, and 4-nonylphenols and average rates of exceeding the EQS were 58.3%, 36.4%, 91.5%, 99.9%, 74.8%, and 49.4%, respectively. The detailed emission inventory of each water body in the basin has been made. Potential sources of PSs were searched via the matrix formed and a total number of 420 basic and supplementary measures were proposed to improve the water quality of the sub-basin.