In the Mediterranean Sea, two critical issues affect marine benthic biocenosis: sedimentation and the increasing trend in marine biodiversity loss. These processes are very marked along the western side of the Calabrian coastline, where siltation is one of the main reasons for the regression of Posidonia beds in the regional coastal waters. This study investigates the relationships between the geomorphological features of the debris source areas, represented by fluvial basins, and the distribution of Posidonia meadows. So, a concise geomorphological study of the Tyrrhenian fluvial basins with an area greater than 200 km2 was carried out, and we correlated the results with the mapping of the meadows in Calabria’s Tyrrhenian waters. Furthermore, to assess the increased level of burial in a Posidonia oceanica meadow and its health state over time, a program of Posidonia monitoring was undertaken between 2000 and 2010 in a test area located in the Marine Regional Park of Isca (Calabria, Southern Italy). The results of this survey highlighted that, at the beginning of the study period, the silting rate of 4–5 cm/year saw the meadow suffer a reduction in its photosynthetic ratio with a mortality rate of 50%. The siltation rate reached 12 cm/year in 2010, and the meadow began to disappear. Therefore, marine pollution via sedimentation represents a serious factor in the regression of Posidonia oceanica meadows and enhances the risk of a gradual loss of marine biodiversity.