Three recently acquired eastern Mediterranean cores containing Late Quaternary sediments display a marked faunal contrast between the Holocene and older sapropels. It is suggested that the absence of neogloboquadrinids in the Holocene sapropel and their abundance in older sapropels reflect differences in food availability related to the extent of development of a deep chlorophyll maximum layer (DCM) and the intensity of “new” primary production associated with this layer. The depth of such a layer, which consists of phytoplankton with a characteristic taxonomic composition, is determined by the vertical hydrodynamical structure. During deposition of the older sapropels, the pycnocline was apparently positioned well above the base of the euphotic layer, a situation that favors a pronounced DCM and an associated relatively high rate of new production. Shallowing of the pycnocline implies a relatively low density of the Mediterranean Intermediate Water (MIW). On the other hand, during deposition of the Holocene sapropel the pycnocline had apparently vanished due to termination of MIW formation.