Major climatic fluctuations that affected Europe and the North Atlantic from the Medieval Climate Anomaly to the Little Ice Age (approximately 500–1850 AD) had significant effects on hydrological regimes in North Africa. In Tunisia, these variations in the water cycle resulted in substantial changes in precipitation, fluvial dynamics, and consequently sediment and nutrient inputs into coastal systems. The Ghar El Melh lagoon, now isolated from the Gulf of Tunis, and the Khneiss lagoon provide valuable settings for investigating local responses to these hydroclimatic changes. Historically supplied with water and sediments from the Medjerda River, the Ghar El Melh lagoon, together with the Khneiss lagoon, has recorded the combined effects of climatic variability, deltaic transformation, and progressive anthropogenic influence in the region. Initial results from our multidisciplinary research suggest that fluctuations in the hydrological cycle have strongly influenced sedimentation and the dynamics of benthic communities, particularly foraminifera, which are sensitive bioindicators of environmental stress. As part of our research into past environmental dynamics, we have initiated a multidisciplinary study of the Ghar El Melh lagoon in northern Tunisia and the Khneiss lagoon. This project aims to reconstruct climatic and environmental changes that occurred over the last centuries, a particularly critical period for this sector of the Mediterranean coastline. Preliminary results reveal significant changes in the composition of benthic foraminiferal assemblages, together with notable changes in sedimentary processes. These disturbances are closely associated with major transformations of the hydrosedimentary system of the Gulf of Tunis, particularly the infilling of the Utica Bay and the progressive isolation of the Ghar El Melh lagoon, as well as the recent anthropogenic transformation of the Khneiss lagoon. The Medjerda River, the main river in northern Tunisia, has played a decisive role in this evolution through its substantial sediment inputs. These nutrient-rich sediments have contributed to changes in the trophic conditions of the lagoon and to the development of specific benthic assemblages, particularly among foraminifera.