Point-source measures have been suggested to decrease pharmaceuticals in water bodies. We analyzed 68 and 50 alternatives, respectively, for a typical Swiss general and psychiatric hospital to decrease pharmaceutical discharge. Technical alternatives included reverse osmosis, ozonation, and activated carbon; organizational alternatives included urine separation. To handle this complex decision, we used Multiple-Criteria Decision Analysis (MCDA) and combined expert predictions (e.g., costs, pharmaceutical mass flows, ecotoxicological risk, pathogen removal) with subjective preference-valuations from 26 stakeholders (authorities, hospital-internal actors, experts). The general hospital contributed ca. 38% to the total pharmaceutical load at the wastewater treatment plant, the psychiatry contributed 5%. For the general hospital, alternatives removing all pharmaceuticals (especially reverse osmosis, or vacuum-toilets and incineration), performed systematically better than the status quo or urine separation, despite higher costs. They now require closer scrutiny. To remove X-ray contrast agents, introducing roadbags is promising. For the psychiatry with a lower pharmaceutical load, costs were more critical. Stakeholder feedback concerning MCDA was very positive, especially because the results were robust across different stakeholder-types. Our MCDA results provide insight into an important water protection issue: implementing measures to decrease pharmaceuticals will likely meet acceptance. Hospital point-sources merit consideration if the trade-off between costs and pharmaceutical removal is reasonable.