The Knysna Estuary is the largest clear-water estuary along the coast of South Africa, with a spring-tide prism volume of 19 x l06 m3 and a tidal range of 1.8 m. The tidal flow covers an area of 1827 hectares at HWST. The tidal system is divided into an upper estuary which receives the variable flow of the Knysna River, a lagoon sector and a large marine embayment. The position and magnitude of the salinity gradient varies according to river flow and, in view of this variability, a linear nutrient concentration-salinity relationship (conservatism) is only weakly established, if at all. Urbanisation of the littoral has encroached upon intertidal wetlands and both stormwater and sewage treatment plant flows introduce nutrients into the water column. While these provide localised inputs, their contribution to the nutrient budget of the system compared with that introduced by the tidal prism is small. The overall effect is to sustain the oligotrophy (chlorophyll-a = 2.16 pg/I) of the water column. Total suspended solids introduced via stormwater and stream inflows decrease transparency during summer, and are considered a serious threat to the long-term survival of the extensive eelgrass meadows upon which so much of the nutrient mobilisation depends. Among the heavy metals, lead and cadmium show elevated concentrations in the soft tissues of oysters, but not as yet to dangerous levels. Polynuclear aromatic hydrocarbons are undetectable in the water column and polychlorinated biphenyls are rarely recorded. It is argued that the magnitude of the tidal prism overrides, at present, the impact of nutrients or toxic materials of anthropogenic origin on the water quality of the estuary.