During the late Quaternary the past climatic conditions of southern South Africa underwent fluctuations, influenced by various climatic factors, such as the impacts of both the Indian and Atlantic Oceans, as well as the effects of the southeasterly trade winds and Southern Hemisphere Westerlies (SHW), influenced by changes in orbital parameters. At the same time, this region exhibits some of the most abundant Middle Stone Age (MSA) archaeological sites containing records of Homo sapiens behavioural and technological evolution. Consequently, there is a pressing need for precise climatic reconstructions that can provide climate constraints during the MSA in this area. However, there is a lack of continuous high-resolution climate records covering the majority of the MSA, which spans from ~300 to ~60 ka. In this study, we present data obtained from a marine sediment core (MD20-3592) that spans approximately the last 260,000 (from m8 to 1) aiming to expand the spatial and temporal coverage of available climate archives. This marine sediment core documents both terrestrial and ocean hydroclimate variability because it is strategically positioned close to the South African coastline receiving terrestrial sediments via riverine input as well as being located under the marine influence of the Agulhas Current at the same time. X-ray fluorescence (XRF) core scanning, calibrated with discrete samples analyzed by XRF spectroscopy, was used to determine the variability of the bulk elemental composition of the core over time. Principal component analysis was performed to facilitate the interpretation of the data. Statistical analyses including frequency analysis, gaussian filtering, and wavelet analysis reveal that the regional hydroclimate was affected mostly by local insolation changes caused by orbital precession, and high latitude forcing that varies on timescales associated with orbital obliquity and eccentricity. Increased fluvial input was associated with a high precession index, during times of high local insolation, due to the effects of precession on local convergence and seasonal rainfall. Comparison with regional climate archives confirmed the dominant influence of precession on precipitation in southern South Africa. On glacial-interglacial timescales, lower precipitation observed during glacial intervals could be explained by a northward shift of the Southern Hemisphere Westerlies (SHW) and South Indian Ocean convergence zone (SIOCZ). Finally, the data from core MD20-3592 can provide a climatic context for the appearance of behavioral complexity in South Africa between ~ 120 ka and ~ 50 ka. Humid conditions in the river catchments going through the south coast and south-east coast of South Africa were present at approximately 117 ka, 93 ka, and 72 ka, alternating with dry conditions at approximately 105 ka, 83 ka, and 60–50 ka.