Persistent organic pollutants such as polychlorinated dibenzo--dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are environmental contaminants that have widespread distribution and pose a serious threat to aquatic ecosystems. We conducted a study to quantify the distribution, patterns, and transport of PCDDs and PCDFs along the Pilica River in central Poland under different hydrological conditions to estimate the loads of these compounds and understand their fate in aquatic systems. Water samples were collected at five sampling points along the river that represent a range of hydrological conditions including flooding and stable and low water flows. Reduced river water flow was associated with lower average total and toxic equivalent (TEQ) concentrations of PCDDs plus PCDFs: 33.6 pg L and 4.21 pg TEQ L for flooding; 28.3 pg L and 3.6 pg TEQ L for stable flow; 18.4 pg L and 1.0 pg TEQ L for low-water flow. Similar results were observed for daily loadings of total and TEQ concentrations: the highest values were observed during flooding (331.1-839.4 mg d and 27.8-110.7 mg TEQ d), medium under stable hydrological conditions (55.8-121.0 mg d and 7.7-15.3 mg TEQ d), and the lowest values during low water flow (30.9 and 40.3 mg d and 1.4-2.4 mg TEQ d). The results demonstrate that diffuse sources of pollution play a key role during periods of high water flow (i.e., flooding season), whereas point sources of pollution, including municipal and industrial wastewater treatment plant discharges, mainly determine the PCDD and PCDF concentrations seen during low water periods.