The ‘Cape Flats’ region, situated in the winter rainfall zone of South Africa, is a low-lying tombolo underlain by recent fluvial and aeolian sands and characterised by numerous small lakes and wetlands. One of these is Princessvlei, a eutrophic, freshwater coastal lake. The lake lies in an inter-dunal depression encroached on in the more recent past by high-density residential, industrial and agricultural land uses. A 210-cm core extracted from the lake periphery yielded high diatom fossil concentrations for the upper 174 cm. Princessvlei appears to oscillate between two ecologically stable states, namely, a state characterised by clear water, oligotrophic, benthic communities and a turbid state dominated by eutrophic, planktonic species. The two stable ecological states are interpreted to be a function of the relative dominance of catchment precipitation or groundwater influx which augments the open water conditions. From 2600 to 1500 cal. BP (173–135 cm), the system is predominantly turbid with greater moisture availability before a relatively rapid development of oligotrophic and dilute conditions from 1300 to 610 cal. BP (135–30 cm). A brief period of deeper water depths and meso-eutrophic conditions is observed between 550 and 445 cal. BP (23–13 cm). Following a short-lived hiatus, poly-hypertrophic, alkaline species are abundant in the top 10 cm coinciding with European colonisation in the region from the 17th century.