The modern Mediterranean Sea is oligotrophic, yet its sediment record contains layers of organic-carbon-rich sapropels at 21 ky (precessional) spacing that imply periods of elevated paleoproductivity that approached the high productivities of modern upwelling systems. Resolution to this paradox is provided by lines of evidence suggesting that the mode of primary productivity changed from one dominated by algae to one during times of sapropel deposition in which photosynthetic bacteria were important. We have made a high-resolution comparison of the organic carbon and nitrogen isotopic compositions of three sapropels and their background sediments in a 3-m sequence that corresponds to 1001 to 946 ka. Organic δ13C values systematically increase from − 26‰ to − 21‰ and δ15N values systematically decrease from ∼4‰ to < 0‰ as organic carbon mass accumulation rates increase in the sapropel layers. The increase in carbon isotope values mirrors the increases in primary productivity and associated organic matter export indicated by the increased mass accumulation rates. The decrease in nitrogen isotope values implies major contributions of nitrogen-fixing cyanobacteria to the total marine productivity. The precessional minima with which sapropels coincide were times of wetter climate that stratified the surface Mediterranean Sea, increased delivery of soil-derived phosphorus, and evidently amplified microbial primary production. Our high-resolution study reveals several relatively rapid excursions into and out of the high-productivity mode that suggest that sapropel deposition was a climate-sensitive surface-driven phenomenon that was not accompanied by basin-wide stagnation.