The Mediterranean Sea is a critical marine environment and resource for Europe, Africa, and the Middle East. Due to its narrow connection to the open Atlantic Ocean, the Mediterranean’s nutrient reservoir is vulnerable to change, with arguments that it is already highly perturbed by human activities. We use the nitrogen (N) isotopes of fossil-bound organic matter (1) to investigate the relationship of the modern Mediterranean Sea to its background Holocene conditions and to previous interglacial periods, and (2) to reconstruct the response of the Mediterranean Sea nitrogen cycle to the glacial-interglacial cycles and other climatic changes. Contrary to previous assessments, our fossil-bound N isotope measurements indicate that the modern Mediterranean N reservoir is predominantly of natural rather than anthropogenic origin and reflects typical interglacial conditions. Over recent glacial cycles, N₂ fixation varied to balance N loss in the shelf sediments, which, in turn, varied in response to sea level change. Superimposed on the glacial-interglacial changes, the periodic occurrence of organic-rich sediments known as “sapropels” has elicited interpretations of extreme environmental change. We show that sapropels arose from freshwater-driven slowing of the Mediterranean’s lagoonal overturning circulation and deep-water formation, which allowed the silled eastern basin subsurface to become oxygen-deficient. Conditions at the surface were largely unaffected, except during episodic eastern basin flushing events that delivered silicate and excess phosphorus to surface waters, driving blooms of N₂ fixer-bearing diatoms that were efficiently preserved in the sapropels. In sum, over glacial-interglacial cycles and during sapropels, biogeochemical changes in the Mediterranean Sea's upper water column were modest, but small chemical reservoirs and bathymetric restrictions to ventilation led to dramatic changes in the nitrogen isotopes and other proxies in Mediterranean sediments.

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