This study presents the level of polychlorinated biphenyl (PCB) pollution in the transboundary Ile River in 2015, 2018, 2019, 2023, and 2024. PCB contamination of water, as well as the presence of a large number of individual congeners, including strictly controlled ‘marker’ and dioxin-like congeners, were detected along the entire length of the river within Kazakhstan. Water samples were analyzed using a Chromos GH-1000 gas chromatograph. Significant interannual variability of river water contamination and a noticeable decrease in 2023 and 2024 compared to the previous periods have been identified. The study examined the PCB concentration transformation in the Ile River, from the transboundary section to the river’s confluence with Lake Balkhash, assessing not only fluctuations in total PCB concentration, but also their congener composition. The main natural and anthropogenic PCB sources and factors causing the transformation of the toxicant along the river course were identified. The total amount of transboundary PCB discharge both into Kazakhstan and into Lake Balkhash was calculated. The results can be used by state and local environmental protection agencies for the development of measures to protect rivers from pollution by these highly toxic pollutants, which is in line with the requirements of the Stockholm Convention on POPs.