This study reports the results of geochemical investigations carried out in the Strait of Sicily (Central Mediterranean Sea) during the oceanographic cruise BANSIC 2000, focusing on the area around the Pantelleria Island. We evaluate the interface processes between dissolved phase and suspended particulate matter in the water columns on the basis of Y/Ho ratio and rare earth elements and yttrium distributions that are suitable to trace the occurrence of different water layers in Central Mediterranean Area. The main source of trace elements to the sea water system was recognized in the atmospheric fallout, while different scavenging mechanisms among Y and rare earth elements occur. Cation exchange at the dissolved phase–suspended media interface is driven by their external electronic configurations as monitored through the Y/Ho ratios, shape, and amplitude of the tetrad effects calculated along the water columns. The shape and amplitude of the tetrad effects in bottom waters suggest that the preferential Y scavenging from deep water layers depends on the hydrothermal activity in the seafloor. Here, Y is surface-complexed through the formation of inner-sphere complexes; Ho and other heavy rare earth elements are sorbed onto suspended particulate matter surfaces as weak outer-sphere complexes; these materials have a montmorillonite like nature; and preferential incorporation medium rare earth elements in crystal structures of biogenic carbonates is suggested by the relationship between the Eu anomaly and the nutrient contents of water masses.