Recurrent deposition of organic-rich sediment layers (sapropels) in the eastern Mediterranean Sea is caused by complex interactions between climatic and biogeochemical processes. Disentangling these influences is therefore important for Mediterranean palaeo-studies in particular, and for understanding ocean feedback processes in general. Crucially, sapropels are diagnostic of anoxic deep-water phases, which have been attributed to deep-water stagnation, enhanced biological production or both. Here we use an ocean-biogeochemical model to test the effects of commonly proposed climatic and biogeochemical causes for sapropel S1. Our results indicate that deep-water anoxia requires a long prelude of deep-water stagnation, with no particularly strong eutrophication. The model-derived time frame agrees with foraminiferal δ13C records that imply cessation of deep-water renewal from at least Heinrich event 1 to the early Holocene. The simulated low particulate organic carbon burial flux agrees with pre-sapropel reconstructions. Our results offer a mechanistic explanation of glacial–interglacial influence on sapropel formation.