Comparison of calcareous dinoflagellate cyst assemblages with Ba, Al, Mn, and Fe records from three sediment cores collected in the eastern Mediterranean Sea indicate that calcareous dinoflagellate cysts are generally resistant to postdepositional dissolution. Cyst association changes during and after sapropel S1 formation can therefore be closely related to variability in surface water productivity. Two groups of cysts are defined: those having highest abundances within the sapropelic and postsapropelic sediments. The temporal cyst distributions suggest increased freshwater input mainly from the Nile and a shallowing of the pycnocline as the most important processes increasing nutrient concentration in the photic zone, thus leading to increased productivity and organic carbon fluxes during sapropel formation. Furthermore, a general warming trend at the beginning of S1 formation and a slight salinity decrease are reconstructed.