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A 12-month survey investigated seasonal variations in the vertical distribution of benthic microalgal biomass in relation to major factors potentially controlling their dynamics in the subtropical temporarily-open Mdloti Estuary, KwaZulu-Natal, South Africa. Benthic microalgal chl-a concentrations in the upper 5 cm of sediment ranged from 259 mg m −2  to 977 mg m −2  during the closed phase, and from 6.7 mg m −2  to 305 mg m −2  during the open phase. Significant differences were obtained between sampling sites and among seasons. A distinctive trend of increasing chl-a biomass in the deeper layers of the sediment was noted from the upper reaches (head) to the lower reaches (mouth) of the estuary. Chl-a biomass was virtually homogeneously distributed throughout the upper 5 cm of sediment in the lower reaches. Results suggest that benthic microalgal cells not only exhibited diel rhythms of vertical migration but were actively re-suspended into the water-column of the Mdloti Estuary. While a decrease in salinity, temperature and K d  favoured an increase in benthic microalgal chl-a biomass in the upper 5cm sediment, nutrients in the overlying water had no significant impact on the biomass. Results further indicate a physiologically healthy community at all sites during the open phase, as compared to the closed phase of the estuary. During the closed phase, the pheopigment to chl-a ratio indicated an actively growing community in the upper reaches and a “stressed” community in the middle and lower reaches. Thus, the large amounts of “buried” benthic microalgal chl-a biomass found in the upper 5 cm of sediment may represent an important stock of potential primary producers in temporarily-open estuarine systems like the Mdloti.

Seasonal Variations in the Vertical Distribution of Benthic Microalgae in the Upper Sediment of the Mdloti Estuary, South Africa