The data refer to fifteen-day and monthly measurements of sinking particulate matter in the marine areas of the northern Aegean, Cretan, Ionian Seas and the Levantine/northeastern Mediterranean. The collection instruments were PPS3/3 Technicap sediment traps with collection areas of 0.125 m² and 12 receiving cups. The locations and corresponding depths of the trap deployments for the different areas are as follows: Historical biogeochemical flux data for the time period 2015: A) Northern Aegean Sea (station M2, Athos Basin): 39°58.16′ N, 24°43.48′ E; d...