Despite the development of organic farming, the demand for mineral fertilizers is still high. Processes of fertilizer production are water-consuming, which is why factories are often located near large rivers. Such facilities should be monitored in detail because they might pose a threat to water quality. The aim of this study was to analyse the impact of a nitrogen fertilizer factory chemical wastewater treatment plant (CWTP) on the water quality of nearby river-lake systems. Potential contamination could indicate installation defects. Six floodplain lakes were selected for analysis: three located within the embanked area and three outside the embanked area, all close to the CWTP. Two similar lakes 30 km upstream were chosen as controls. Water samples were taken monthly from March to November 2022. We analysed pH, electrical conductivity (EC), the content of Cl−, total nitrogen (TN), NH4+, NO3−, total phosphorus (TP), PO43−, dissolved organic carbon (DOC), Ca2+, K+, Mg2+ and Na+. Statistical analysis indicated that the canal that drains, among others, the cooling towers wastewater, might have an impact on the nearby lakes, significantly increasing their content of Cl− and Na+. On the other hand, the concentration of NH4+ was significantly higher in the lakes located downstream of the CWTP, although they did not have any surface connection with the CWTP reservoir. This fact and NH4+-polluted water seeping under the dike indicate that the CWTP reservoir might be leaking. Further research on underground water is required to establish whether the CWTP reservoir is properly secured. It is extremely important because the CWTP is located in the Vistula River valley, which supplies drinking water to almost 2 mln people. Any damage to the reservoir, e.g., during a flood, would lead to an ecological disaster involving not only the Vistula but also the Baltic Sea, affecting millions of people.