ABSTRACT:  The vast majority (73%) of South African estuaries are temporarily-open systems. There is virtually no information available on their trophic functioning, particularly at the lower levels of the food web. A whole-year survey was carried out toinvestigate variations in the biomass of phytoplankton and microphytobenthos in relation to major factors potentially controlling their dynamics in a subtropical temporarily-open estuary. Microphytobenthic chlorophyll a (chl a)concentrations ranged from 75 to 480 mg m^-2, while phytoplankton biomass varied between 0.09 and 8.6 mg chl a m^-3. Areal chl a concentrations in the sediment (microphytobenthos) were typically 1 to 2 orders of magnitudehigher than in the water column (phytoplankton). The vertical attenuation coefficient in the water, K_d, varied between 0.94 and 28.9 m^-1. Dissolved inorganic nitrogen to phosphorus molar ratios (DIN:DIP) varied between 0.3and 127. The results suggest that nutrients rather than light might have limited phytoplankton growth during the closed phase of the estuary, since K_d values were lowest during this period. On the other hand, light rather than nutrientsmight have limited phytoplankton growth during the open phase, since nutrient concentrations in the water column were very low prior to the opening of the estuary at the mouth. The marked increase in phytoplankton biomass at the onset of the open phasefurther supports the hypothesis that phytoplankton cells might have been nutrient-limited during the closed phase. Resuspension by freshwater inflow may have also contributed to this increase. Microphytobenthic standing stock exhibited strong seasonalfluctuations, with the lowest values coinciding with the open phase. However, unlike phytoplankton, benthic microalgal biomass did not appear to be inhibited by either low nutrients or light availability.