South African coastal lake sediments provide an excellent opportunity to investigate environmental changes such as sea level and climate variability during the Holocene Period. In this study we present a sediment record from the coastal lake Groenvlei located in the southern Cape region which is part of South Africa's year-round rainfall zone. In order to improve the understanding of palaeoenvironmental changes in this region, we provide a high-resolution multi-proxy data set derived from geochemical, mineralogical, isotopic and granulometric analyses. The age-depth model is based on 14C and 210Pb dating and reveals a basal age of 4210 + 200/− 120 cal BP. Differences in the mineralogical composition of deposited carbonates reflect changes in the past lake water chemistry, probably caused by variations in both sea level and climate. Compared to the present, mostly drier conditions and a greater marine influence due to a higher sea level are inferred for the period between 4210 and 2710 cal BP. However, the record also indicates the occurrence of short humid phases during this time, which were probably associated with heavy rainfall events. A transition layer was deposited between 2710 and 1210 cal BP, probably as a result of reworking of sediment. During this time, the lake passed through a major change finally turning into a freshwater system from at least 1210 cal BP until the present. Our data indicate that the marine influence on the lake decreased due to a lower sea level and climate became generally more humid after 1210 cal BP probably resulting in a greater lake-internal and -external bioproductivity. Based on a comparison with other palaeoenvironmental studies from South Africa, our record suggests a prevailing winter rainfall seasonality at the southern Cape coast between 4210 and 2710 cal BP and a stronger influence of the summer rainfall zone from 1210 cal BP onwards.