Coastal zones are under rising anthropic pressures, unchaining unprecedented changes in their ecosystems. Due to the efforts made to monitor these changes on a big scale, there is a rising awareness of human impact on these regions. This is motivating the establishment of new Marine Protected Areas. However, traditional tracking methods require important investments of time and resources. In consequence many of these reserves lack proper tracking. Remote sensing is set to be one of the most cost-efficient tools for monitoring great extensions of seabed in shallow water regions. This study shows the effectiveness of Sentinel-2 mission monitoring Els Freus de Ibiza y Formentera Marine Reserve. This is accomplished by generating and testing a Satellite Derived Bathymetry (SDB) and a benthic habitat cartography. Resulting SDB had an RMSE ranging from 2 to 3 m. Overall accuracies of the cartography ranged between 79 and 86%. These results are comparable to other remote sensing studies and even to in situ measurements. In conclusion, this work shows that Sentinel-2 platform could be useful for Marine Protected Areas management, lowering monitoring costs on big scales.