The southern Cape coast, South Africa, is sensitive to climate fluctuations as it is influenced by different atmospheric and oceanic circulation systems. Palaeoecological evidence of Holocene climate variations in this region is presently limited. Here, we present a lake sediment record spanning approximately the last 670 years from Eilandvlei, a brackish coastal lake situated mid-way between Cape Town and Port Elizabeth. The results from geochemical and sedimentological analyses point to an increase in minerogenic sediment input from the catchment starting around ad 1400. Changes in the seasonal distribution of rainfall during the Little Ice Age may have altered river discharge and increased erosion rates and fluvial sediment transport in pre-colonial times. A rising mean lake level, possibly associated with an altered water balance or relative sea-level rise, may offer an explanation for the deposition of finer sediments. After ad 1450, reduced burial flux of elements associated with autochthonous sediment formation may have resulted from ecological changes in Eilandvlei. Enhanced sedimentation rates, increasing carbon, nitrogen, phosphorous and biogenic silica concentrations, as well as high concentrations of proxies for allochthonous sediment input (e.g. aluminium, titanium, zirconium) point to increasing sediment and nutrient flux into Eilandvlei from the late nineteenth century onwards. The most likely factor involved in these recent changes is land-use change and other forms of human impact.