Dark organic-rich layers (sapropels) have accumulated in Mediterranean sediments since the Miocene due to deep-sea dysoxia and enhanced carbon burial at times of intensified North African run-off during ‘Green’ Sahara Periods (GSPs). The existence of orbital precession-dominated Saharan aridity/humidity cycles is well known, but lack of long-term, high-resolution records hinders understanding of their precise relationships with environmental and hominin evolution. Here we present continuous, high-resolution geochemical and environmental magnetic records for the Eastern Mediterranean that span the past 5.2 million years, which reveal that organic burial in sapropels intensified 3.2 Myr ago. We deduce that fluvial terrigenous sediment inputs during GSPs doubled abruptly at this time, whereas monsoon run-off intensity remained relatively constant. We attribute the increase in sediment mobilisation to an abrupt non-linear North African landscape response associated with a major increase in arid:humid contrasts between GSPs and intervening dry periods. This likely limited hominin (and other animal) inhabitation of, and migration through, the Sahara region to GSPs only.