North African greening phases, during which large rivers ran through the Sahara Desert, occurred repeatedly during the Quaternary and are regarded as key periods for the development of past human populations. However, the timing and mechanisms responsible for the reactivation of the presently dormant fluvial systems remain highly uncertain. Here we present hydroclimate changes over the past 160,000 years, reconstructed from analyses of the provenance of terrestrial sediments in a marine sediment record from the Gulf of Sirte (offshore Libya). By combining high-resolution proxy data with transient Earth system model simulations, we are able to identify the various drivers that led to the observed shifts in hydroclimate and landscapes. We show that river runoff occurred during warm interglacial phases of Marine Isotope Stages 1 and 5 due to precession-forced enhancements in the summer and autumn rainfall over the entire watershed, which fed presently dry river systems and intermittent coastal streams. In contrast, shorter-lasting and less-intense humid events during glacial Marine Isotope Stages 3 and 4 were related to autumn and winter precipitation over the Libyan coastal regions driven by Mediterranean storms. Our results reveal large shifts in hydroclimate environments during the last glacial cycle, which probably exerted a strong evolutionary and structural control on past human populations, potentially pacing their dispersal across northern Africa. The presence of large rivers in North Africa critical for Quaternary human migrations were controlled by a combination of orbital forcing and Mediterranean storminess, according to terrestrial proxy records from a marine core off Libya integrated with paleoclimate modelling.