The concentrations and behaviour of 105 different active pharmaceutical ingredients (APIs) in the aqueous phase of sewage water within a municipal sewer collection system have been investigated. Sewage water samples were gathered from seven pump stations (one of which was located within a university hospital) and from sewage water treatment influent and effluent. The targeted APIs were quantified using a multi-residue method based on online solid phase extraction liquid chromatography tandem mass spectrometry. The method was thoroughly validated and complies with EU regulations on sample handling, limits of quantification, quality control and selectivity. 51 APIs, including antibiotics, antidepressants, hypertension drugs, analgesics, NSAIDs and psycholeptics, were found frequently within the sewer collection system. API concentrations and mass flows were evaluated in terms of their frequency of detection, daily variation, median/minimum/maximum/average concentrations, demographic dissimilarities, removal efficiencies, and mass flow profiles relative to municipal sales data. Our results suggest that some APIs are removed from, or introduced to, the aqueous phase of sewage waters within the studied municipal collection system.