Inspired by the study conducted in the Orbetello lagoon (Italy), we developed a versatile hydrodynamics model which can be used to help prevent hypoxia of the fauna and flora in the bays of French Polynesia. The model represents the first phase of a multi-step strategy. This first step allows us to determine five critical points where to perform a seasonal measurement campaign of the water level and currents. The measurements, which represent the second phase of the project, will permit to define the most effective strategy to optimize the hydrodynamics flow by the mean of water pumps, bottom dragging or reef drilling.