The release of micropollutants in surface water depends on different sources and on different pathways. Through substance flow analysis, this study estimates the annual load of two pharmaceuticals (carbamazepine and sulfamethoxazole) in a catchment area, due to different emission pathways: wastewater treatment plant effluent, combined sewer overflows, and runoff from sludge and manure amended soil. It emerged that wastewater treatment plant effluent is the main emission pathway for carbamazepine (98.5% referring to the total released annual load) and land runoff (98%) for sulfamethoxazole. The study also investigates the parameters (including manure disposed on the land, removal efficiency and combined sewer overflow flowrate) which mostly influence the results, and those which are affected by higher uncertainty. The most uncertain parameters are those determining the fate of pharmaceuticals once in soil and surface water. The study concludes with a comparison between the predicted concentrations in different points of the receiving water body of the two key compounds, modeled with substance flow analysis, and those directly measured in a dedicated sampling campaign. The main discrepancies were found for sulfamethoxazole. Future research focusing on monitoring campaigns under different weather conditions and in different environmental compartments (soil and water) will certainly provide new insights in this kind of study. Display omitted •Prediction of pharmaceutical release in river by different emission pathways•Carbamazepine and sulphamethoxazole selected as key compounds.•Carbamazepine mainly released by wastewater treatment plant effluent.•Sulfamethoxazole mainly released by land runoff.•Uncertainties mainly due to the fate of pharmaceuticals in soil and surface water.