The levels of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and dioxin-like polychlorinated biphenyls (dl-PCBs) in the Pilica River and Sulejów Reservoir were found to be 46% higher during the flood season than during stable flow periods. In addition, PCDD/PCDF and dl-PCB mass loads increased by 5- to 12-fold and by 23- to 60-fold for toxic equivalency (TEQ) during flooding. The Sulejów Reservoir was found to play a positive role in reducing PCDD, PCDF and dl-PCB transport within the study period, with reductions ranging from 17 to 83% for total concentrations, and 33 to 79% for TEQ. Wastewater Treatment Plants (WTPs) were not efficient at mass concentration removal, with small displaying the least efficiency. WTPs discharge pollutants into the aquatic environment, they also produce sludge that requires disposal, similar to reservoir sediments. Sludge- or sediment-born PCDDs, PCDFs and dl-PCBs may be removed using phytoremediation. The cultivation of cucumber and zucchini, two efficient phytoremediators of organic pollutants, on polluted substrate resulted in a mean decrease in PCDD + PCDF + dl-PCB TEQ concentrations: 64% for cucumber and 69% for zucchini in sludge-amended soil, and by 52% for cucumber and 51% for zucchini in sediment-amended soil.