Managing combined sewage systems in large cities discharging to coastal waters, often bearing recreational activities, remains a challenge. Studying the impacts of such discharges requires the development of specific models. Hydrodynamic and water quality modelling of coastal waters employs numerical methods and algorithms, leading to the design of complex models which require expert use. The use of such models as decision support tools to simulate discharge impacts and define adequate corrective measures could represent a key part in meeting this challenge. In this paper, the authors describe the work undertaken to develop an operational decision support system (ODSS) methodology aiming to enable wastewater utilities' non-expert staff to carry out user-friendly scenario analysis based on computational fluid dynamics simulations. This article depicts the application and validation of the ODSS to the combined sewage system and the Tagus estuary of the city of Lisbon in Portugal. The ODSS was used for simulating the effects in the receiving coastal waters of a discharge caused by a scheduled maintenance operation in the sewage infrastructure. Results show that the use of such ODSS by non-expert staff increases their decision capabilities and knowledge of the wastewater utility's contribution to reducing negative impacts of sewage discharges on the receiving water bodies.