This work investigates the hydrodynamic response of two small and shallow bays located in the Ebro Delta, in order to solve the problems affecting mussel farms, such as the high temperatures reached in the summer period (>28 °C), causing the death of these bivalves, and the limited water renewal that causes anoxia within the bay. Nature Based Solutions are described focusing on two aspects: one, modifying the flow of these drainage channels, increasing the arrival of freshwater to the bays; and two, opening a gap in the sand bars so that there is a flow of sea water in and out through the innermost zone, which is where both bays have greater problems of water renewal. The impact of those solutions simulated with the Regional Oceans Modeling System (ROMS), consist of a set of nested domains that use CMEMS-IBI data for the initial and open boundary conditions (coarser domain). To validate the numerical model, data from in situ campaigns have been used for one full year (2014) for Alfacs Bay, and for the summer period (July-August 2017) for Fangar Bay. In addition, the Sea Surface Temperature (SST) is also studied as an indicator to reduce the mortality problems of mussels, but the results obtained do not reduce this variable. What the results do show is a decrease in residence time in both bays for both experiments, with the increase in flow being more viable than the increase in sand bar breakage.