The hydropower production, water supply and aquaculture services of the Itaparica Reservoir are of immense importance for the Brazilian Northeast. Uncontrolled water resources consumption (e.g. irrigation, water supply), climate and land use change effects deteriorated the water quantity and quality in the reservoir, leading to socio-economic and environmental problems. In this work, a depth-averaged shallow water model was set up for the Icó-Mandantes Bay, one major branch of the reservoir, using the open TELEMAC-MASCARET system. The aim was to assess the impacts of the newly built water diversion channel, as well as the effects of a flood and tracer transport from an intermittent tributary, both located in the bay. An alternative approach to estimate the water retention times was additionally implemented. The simulations showed that though the diversion channel did not significantly influence the hydrodynamics of the bay, it is necessary to continuously monitor water quality parameters in the withdrawal, especially during rainy periods after droughts, because of the nutrient inputs from the tributary and the overflows of the nearby drainage systems. Management measures adapting to the continuously changing natural conditions and anthropogenic impacts are thus indispensable and the model presented can be a valuable supporting tool for this purpose.