Zeekoevlei is the largest freshwater lake in South Africa and has a century-long history of anthropogenic impact that caused hyper-eutrophic conditions. We used biomarkers (alkanes and pigments), stable isotopes (delta C-13 and delta N-15), rates of primary palaeoproduction and total inorganic carbon (TIC) accumulation rates in the lake sediments to investigate changes in plankton and macrophyte communities in response to anthropogenic activities in this shallow lake. Specific alkanes (I C-15 pound,C-17,C-19, pristane, phytane and n-C-29/n-C-17 ratio) and pigment (chlorophyll a, beta,beta-carotene, echinenone, fucoxanthin and zeaxanthin) concentrations in lake waters indicated the present-day hyper-eutrophic condition and seasonal fluctuations of cyanobacteria, zooplankton and diatom populations. Eutrophic conditions were initiated in the lake with the start of recreational activities and construction of a sewage treatment plant in the early 1920s. The lake transformed from a eutrophic to a hyper-eutrophic waterbody following damming, pondweed eradication and accelerated catchment-derived nutrient input. The change in lake trophic state was recorded by a sharp decline in the terrestrial to aquatic ratio (TAR) of specific n-alkanes, low carbon preference index (CPI) and increased delta C-13 values in the sediment core. In addition, the aquatic macrophyte n-alkane proxy (P-aq) values (similar to 1) indicated a slow takeover by floating macrophytes after the eradication of submerged pondweeds in 1951. Elevated n-alkane (I C-15 pound,C-17,C-19), total alkane and pigment (chlorophyll a, beta,beta-carotene, zeaxanthin and zeaxanthin to beta,beta-carotene ratio) concentrations, low delta N-15 values and low TIC accumulation rates in the upper middle section of the core indicated the beginning of intense cyanobacterial blooms after the dredging in 1983. Although the cyanobacterial population has decreased in recent years, hyper-eutrophic conditions are reflected by low CPI < 0.04 and TAR < 1 values at the top of the sediment core.