Flood events are dependent on meteorological conditions but also depend on several other factors that are case specific, with relevance for reservoir operation. Hydrological and hydrodynamic models are valuable tools for understanding complex river hydrodynamics during flood events. These tools have been applied to improve understanding of the causes for an urban flood event that occurred between 9 and 11 January 2016 in the Mondego river basin, at Coimbra city (Portugal). Seven different factors that can, independently, influence the river flow at the study site were identified: three of them can be associated with the operational discharge schemes of the three upstream dams; two factors with the runoff flows from uncontrolled contributing sub-basins; another one related to discharge measurement uncertainty at a downstream dam; and finally, the seventh studied factor was sedimentation occurring in the main channel of the flooded river stretch. Hydroinformatic tools were applied in different scenarios allowing the characterization and identification of each one of the identified key factors responsible for the flood event. A proposal for a flood early warning system is presented based on the knowledge resulting from the studied flood event.