The Mngazi estuary, a near pristine and wave-dominated estuary located on the subtropical east coast of South Africa, requires careful management to ensure that land use does not alter its ecological function. The present study investigated the quality and quantity of water in the estuary and related these to the microalgae. There was no evidence of a persistent elevated phytoplankton biomass in the region of the estuary where river water mixed with brackish estuarine water, even during periods when the estuary mouth was open. Nutrients that determined the microalgal distribution were likely to have come from the mineralisation of organic material, which had been deposited in the estuary following pulses in river water. Results indicate that microalgae were P-limited when the mouth was semi-closed and N-limited during the closed mouth phase. Average benthic chlorophyll a, which ranged from 0.3 to 56.8 µg g^–1, was highest in the intertidal middle reaches of the estuary. Organic matter and the proportion of fine sediments (<125 µm) was highest in these sediments. A conceptual model was developed to predict the response of the estuary if further changes in the quality and quantity of river water entering the estuary were to occur.