The relationship between microphytobenthic biomass, community structure and physico-chemical conditions was studied in the Van Stadens Estuary, South Africa. Quarterly sampling was conducted in 2003. Temporal variation in community structure was explained by the percentage contribution of very fine sand in the sediment and by porewater ammonium concentrations. Microphytobenthic biomass showed strong negative correlations with water column salinity and sediment redox potential, and a positive correlation with water column soluble reactive phosphorus concentration. Temporal variation in mouth condition, sediment structure and nutrient availability changed biomass and community structure but there was little spatial variability. During the quarterly sampling of this study, microphytobenthic biomass was higher during open mouth conditions (1.43 ± 0.14–3.64 ± 0.94 μg g −1 sediment) than under closed conditions (0.25 ± 0.08–1.88 ± 0.22 μg g −1 sediment). The estuary was sampled weekly immediately following a mouth breaching event, physico-chemical conditions and microphytobenthic biomass were measured. Biomass did not decrease following mouth breaching and ranged between 0.25 ± 0.02 and 0.56 ± 0.10 μg g −1 sediment. This is contrary to other studies on South African intermittently open estuaries and indicates the importance of site specific data and detailed descriptions of the opening event.