In recent decades, Mediterranean benthic communities have undergone significant changes in composition and distribution, largely attributed to global warming. Porifera represent a key group for detecting environmental change, with some species declining and others expanding their range. This study compares present and past sponge diversity at three Mediterranean areas: one site along the Portofino Promontory (Ligurian Sea), the rocky cliffs of Montecristo Island (Tuscan Archipelago), and a semi-submerged sea cave in “Parco Sommerso di Gaiola” (Naples). The same sampling methods from earlier studies were applied. At the Portofino site, squares (400 cm² each) were collected along a vertical transect (0–20 m). At Montecristo, samples were visually selected between 0 and 40 m depth. In the cave, sampling was conducted using quadrats, adapted to cavity morphology and light gradients. At Portofino, 68 species were recorded in 2023 compared to 114 in 1976, with only 43 common species. Species richness declined in all depth intervals except the deeper one. At Montecristo, species richness increased from 27 (1980–1981) to 40 (2019–2020), but only 13 species were shared, indicating a substantial turnover in species composition over four decades. In the cave, species number slightly increased (69 in 1960 to 72 in 2023), yet only 27 species persisted, and sponge cover declined from 55% to 25%. Overall, over a multi-decadal timespan (40–63 years), all sites (Portofino Promontory; Montecristo Island and the Gaiola MPA cave) show a complete shift in sponge diversity, a reduction in overall abundance, and a change in the growth forms, with a decline in massive species and an increase in encrusting forms. These patterns suggest that anthropogenic impacts, together with ongoing climate change, have contributed to the decline and transformation of sponge communities in the Mediterranean Sea.