This study investigates the intricate dynamics of siliceous plankton species within the open marine regions of the Greek Seas, focusing on their seasonal and spatial variability. For this purpose, vertical export fluxes of diatoms (DtF), silicoflagellates (SF), and radiolaria (RF) were analyzed in three sediment trap time series obtained from the North Aegean, Cretan, and Ionian Seas. Special attention was given to diatom assemblages, resulting in the estimation of the DtF community structure and diversity for each studied site. Diatom flux values reached 353.9 × 103 valves m−2 day−1, 77.7 × 103 valves m−2 day−1, and 42.4 × 103 valves m−2 day−1 in the North Aegean, Ionian, and Cretan Seas, respectively. SF maxima were 1309.8 × 103 skeletons m−2 day−1 in the North Aegean Sea, 35.2 × 103 skeletons m−2 day−1 in the Ionian Sea, and 11.9 × 103 skeletons m−2 day−1 in the Cretan Sea (South Aegean Sea). RF values reached 13.9 × 103 radiolaria m−2 day−1, 11.9 × 103 radiolaria m−2 day−1, and 5.4 × 103 radiolaria m−2 day−1 in the North Aegean, Ionian, and Cretan Seas, respectively. The North Aegean Sea exhibited significantly higher mean total fluxes, particularly for diatoms, driven by the north-to-south oligotrophy gradient, which was influenced by riverine inflows and the nutrient-rich Black Sea water. In the Cretan and Ionian Seas, convective mixing and atmospheric deposition, especially during increased rainfall (precipitation) events, were identified as primary drivers for the increased siliceous plankton fluxes recorded in the late winter–spring months. Diatom communities were dominated by Naviculales and Fragilariales; the prevalence of the former in the North Aegean Sea is likely linked to the higher nutrient levels in its upper photic zone, as Naviculales includes species with a high affiliation to nutrient enrichment.
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