The biogeochemistry of the following elements Al, Fe, Sibio, POC, PNtot, Cabio, Sorg, P and Mn has been studied within waters of the Cretan Sea in March and September 1994, as part of the PELAGOS project. Particulate aluminosilicate concentrations, exemplified by Al, are very low (<1 μgl−1) especially in the upper waters. Higher concentrations occur below 200 m, especially at depths of 200 m and 500–700 m in the central and eastern areas, and are thought to result from sediment injections from the shelf edge and slope. The results for Sibio, Cabio, P and Sorg show much higher concentrations within the photic waters. Temporal and spatial high concentrations in these waters closely relate to the existence of cyclonic eddies on the east and west sides of the sea, while low concentrations are associated with an intervening anticyclonic eddy. However in September, discharge of Black Sea Water in the west sufficiently suppresses the thermocline to prevent upwelled water from reaching the surface and hence these substances are prevented from forming. Particulate Fe (expressed as Feexcess) concentrations show much higher concentrations relative to Al in September, and are thought to result from additional atmospheric inputs. The low particulate Mn concentrations in the upper water compared with deeper waters are considered to be a product of photoinhibition of MnOx precipitation from Mn(II). An attempt has been made to assess input/output budgets of Al, Ca, Fe and Mn through the Antikithira and Kassos Straits. Much of the outflows leave through the Kassos Strait and, except for Ca, net outflows through the Antikithira Straits are negligible.