Chemical pollution poses a threat to the aquatic environment and to human health. Wastewater treatment plants are the last defensive line between the aquatic environment and emissions of pollutants. This study focuses on identification of most relevant hazardous substances in Estonian municipal wastewater and their fate in the treatment process. During this study, seasonal wastewater and sewage sludge samples were collected from nine municipal wastewater treatment plants and analyzed for 282 hazardous substances, including EU (n = 45) and Estonian (n = 31) priority substances. Results of this study show that several substances that are subject to international restrictions (e.g. Stockholm Convention) are still present in untreated sewage. Wastewater treatment systems that had a greater level of complexity (TEC >5) were more successful in removing hazardous substances. Statistical analyses showed that removal efficiency of organic hazardous substances had significant (p-value <0.05) linear correlation with removal efficiencies of chemical oxygen demand (COD) and total suspended solids (TSS), but a monotonic relationship with operators' competency. This study showed that operators' competency had a strong influence on the stability of the wastewater treatment efficiency and removal of organic hazardous substances.