Concentrations of pharmaceutically active compounds (PACs) in freshwater systems depend on numerous factors such as land use and hydrometeorological conditions. In the Mediterranean, heavy rain events are of particular importance as they highly influence the concentration of micropollutants found in freshwater and are a source of recurrent first foul flushes due to combined sewer overflows (CSOs). In this study, we seek to assess the dynamics of pharmaceuticals during storm events in coastal Mediterranean rivers at a fine scale and to determine their contribution to multicontamination phenomena owing to CSOs. Our results showed that, while dissolved PACs followed the same trend as other contaminants, i.e., they increased significantly during CSOs, PACs in the total fraction did not peak yet maintained their already high concentrations for slightly longer due to their release via CSOs. Pharmaceutical concentrations for both the dissolved and the total fraction were dramatically diluted during the peak river flow. A fine-scale follow-up of PACs dynamics in the total fraction, including the differentiation of sewer overflows from both the right and left river banks, as well as the analyses of a large amount of PACs molecules, allowed us to clearly identify their major sources. While domestic inputs were dominated by nicotine and caffeine, the use of gadolinium (an MRI contrast agent) as a marker, attributed the main source of medical drugs such as tramadol, ibuprofen, and diclofenac to the major public hospital of the region. Thus, identifying major sources of PACs and implementing adapted water treatments directly at those sources would be the most cost-efficient alternative to cope with pharmaceutical drugs in coastal Mediterranean aquatic environments. Moreover, PACs behavior differed depending on the molecules considered and the source of these molecules, but we could not establish a direct link between their behavior and their chemical or physical properties. Our study highlights the importance of monitoring at strategic locations and with a high frequency sampling in order to better understand fate, sources, and behavior of pharmaceuticals in aquatic environments.