The main objectives of the presented study were to quantify the transfer of polychlorinated dibenzo-p-dioxins (PCDDs)/polychlorinated dibenzofurans (PCDFs) (polychlorinated dibenzo-p-dioxins/polychlorinated dibenzofurans) and dioxin-like polychlorinated biphenyls (dl-PCBs) along the river continuum and to evaluate the impact of wastewater treatment plants (WTPs) located in the catchment on the river quality. The samples were collected during the spring (high water flow) and summer season (serene water flow) of 2010. The river samples were collected from five stations located along the lowland Pilica River, including two stations situated above and below the Sulejow Reservoir. At the same time, samples from the outlets of 17 WTPs were collected. As evidenced by the results, the largest WTPs discharged up to 59.09 μg toxic equivalent (TEQ) of PCDDs/PCDFs and dl-PCBs per day during high flow events and up to 26.03 μg TEQ during serene water flows. During the same time, the smallest WTPs released on average 0.81 and 0.70 μg TEQ day−1, respectively. The obtained results have also demonstrated an increase in the TEQ concentration along the Pilica River continuum (from 4.75 to 6.25 pg TEQ L−1). The exception were samples collected below the dam where 63% TEQ reduction was observed compared to samples collected above the reservoir.