Nitrogen isotopic measurements in fossil chlorophyll from late Pleistocene organic-rich sediments (sapropels) in the eastern Mediterranean Sea provide geochemical evidence for stratified, nutrient-depleted surface water and extensive nitrogen fixation. This evidence is reconciled with previous indications of high productivity by invoking a model of sapropel formation in which increased river discharge facilitates development of a specialized phytoplankton population whose annual mass sinking provides the organic flux to generate sapropels. This interpretation is consistent with the widespread occurrence of mat-forming diatoms that thrive in stratified water and can harbor diazotrophic bacterial symbionts, but does not support eutrophication of surface waters by enhanced river runoff or a circulation reversal.