Due to the high sensitivity of southern Africa to climate change, a reliable understanding of its hydrological system is crucial. Recent studies of the regional climatic system have revealed a highly complex interplay of forcing factors on precipitation regimes. This includes the influence of the tropical easterlies, the strength of the southern hemispheric westerlies as well as sea surface temperatures along the coast of the subcontinent. However, very few marine records have been available in order to study the coupling of marine and atmospheric circulation systems. Here we present results from a marine sediment core, recovered in shallow waters off the Gouritz River mouth on the south coast of South Africa. Core GeoB18308-1 allows a closer view of the last ∼ 4 kyr. Climate sensitive organic proxies, like the distribution and isotopic composition of plant-wax lipids as well as indicators for sea surface temperatures and soil input, give information on oceanographic and hydrologic changes during the recorded time period. Moreover, the micropaleontology, mineralogical and elemental composition of the sediments reflect the variability of the terrigenous input to the core site. The combination of down-core sediment signatures and a catchment-wide provenance study indicate that the Little Ice Age ( ∼ 300–650 cal yr BP) was characterized by climatic conditions favorable to torrential flood events. The Medieval Climate Anomaly ( ∼ 950–650 cal yr BP) is expressed by lower sea surface temperatures in the Mossel Bay area and humid conditions in the Gouritz River catchment. These new results suggest that the coincidence of humid conditions and cooler sea surface temperatures along the south coast of South Africa resulted from a strengthened and more southerly anticyclonic circulation. Most probably, the transport of moisture from the Indian Ocean by strong subtropical easterlies was coupled with Agulhas Bank upwelling pulses, which were initiated by an increase in Agulhas Current strength.