Some less developed regions in China like Jilin Province are still facing severe water pollution challenge, due to insufficient recognition of water pollutant discharge (WPD) features and ineffective regulations. In this study aided by input-output analysis, first, water pollutant footprint (WPF) of Jilin was accounted to clarify WPD distribution when meeting local final demand during 2002–2012. Then, total local WPD was investigated from both direct and embodied perspectives. Finally, structural decomposition analysis (SDA) was conducted to analyze the contributions of multiple drivers to changes in regional WPF and local embodied WPD. The results indicate that the regional WPF dominated by internal WPF (over 71%) decreased over 14%. The local embodied WPD mainly driven by exports (over 65%) increased then decreased to the original level. The volume of local embodied WPD was more than twice that of regional WPF induced by the export of tremendous products with intensive WPD. SDA reveals that direct WPD intensity was the principal contributor to offset both regional WPF and embodied WPD, followed by final demand structure that is moving towards a new pattern with less WPD induced. These effects succeeded in reversing the expansion of regional WPF and embodied WPD induced by the final demand volume effect and production structure effect. This study is an initial attempt on investigating region-specific WPD from multiple perspectives. The results offer insights for developing pertinent policies regarding technologies, structure, consumption and trade for regional water pollution control.