The Monastir region constitutes an invaluable reserve in terms of continental and marine biodiversity. However, the water bodies in Tunisia, such as bays, sebkhas and coasts have become the seat of recurrent appearance of extreme phenomena such as red tides or “Harmful Algal Blooms” (HABs), which are generally manifested by the eutrophication of the waters and the proliferation of algae or harmful bacteria. It is in this context we seek to identify and evaluate the phenomenon of eutrophication at the level of water bodies in the Monastir region. Our methodological approach uses new computer technologies, in particular data science, including sophisticated GIS and remote sensing tools. Results show the identification of four main water bodies using the NDWI index namely (i) the lake/sebkha of Monastir on the north-eastern side, (ii) the Sebkha of Moknine on the south-eastern side, (iii) the Sebkha of Sidi El Heni to the west and (iv) the body of water relating to the sea. Also, four degrees of eutrophication classified from very low to very high are determined based on the NDCI index. However, we found that the concentration of the eutrophication is more accentuated on the coast of Sayada and Teboulba, the bay of Dhkila and at the Sahline’ Sebkha level. We have deduced that anthropogenic actions such as the realization of processes and the use of chemicals in agriculture have a considerable effect on this phenomenon.