Hydrodynamics and transport simulations were conducted with the modeling software TELEMAC-2D on Icó-Mandantes bay, a branch of the Itaparica reservoir. The bay has a maximal operational water level amplitude of 5 m and is suffering from eutrophication and algae bloom. Therefore, we investigated low and high water level scenarios with two different high resolution meshes, with the purpose to deeper understand their impact on transport of substances and to improve the watershed management. In particular, nutrient emissions from a hypothetical net cage aquaculture system located in the bay were investigated on half-year cycles. We observed a relevant impact on water quality for a tilapia production of 130 t y−1; i.e. after 6 months' simulation we obtained around 8 μgP L−1 and 6 μgP L−1 at the source of emissions, for low and high water scenarios, respectively.