In Coimbra city, Portugal, the riverbanks have suffered several floods events in the past, due to its hydrological regime, the low slope and consequent lack of capacity of the Mondego River in its final 30 km. The construction of several dams in the upstream part of the river catchment has improved the use of the hydraulic capacity of the river system and reduced the number and intensity of flooding events in Coimbra. Nevertheless, intense rainfall events combined with inadequate procedures of the dam operation rules and lack of monitoring of sediments dynamics can still originate inundation in Coimbra such as those registered between 9th and 11th of January 2016. This work presents modelling scenarios demonstrating the influence of the sediment accumulation into the riverbed and its effect on the water levels. It also presents the influence that piers from a new bridge can have into the river flow dynamics