The southern Namaqua shelf of the Benguela upwelling system, downstream of the Cape Columbine upwelling cell, is frequently subjected to a variety of harmful algal bloom (HAB)phenomena. Here, winds dictate most physical processes that are important to the development of HABs. Toxic algal cell concentrations and distributions, in relation to their respective toxin content,are compared over 2 autumn periods in successive years which exhibited clearly different wind patterns and hydrographic responses. During the first study period (15 March to 6 April 2005), several periods of relaxation from upwelling-favourable winds were associated with poleward nearshore currents and increasing levels of stratification. The phytoplankton community was dominated by dinoflagellates, including Dinophysis spp. and Protoceratium reticulatum, responsible for the production of toxins associated with diarrhetic shellfish poisoning and yessotoxins, respectively. In contrast, the subsequent study period (7 to 23 March 2006) was characterised by persistent upwelling-favourable winds, equatorward near-surface currents, and a cooler, moderately mixed water column. The phytoplankton assemblage was co-dominated by Pseudo-nitzschia spp. and Chaetoceros spp.; domoic acid concentrations corresponded closely with cell concentrations of Pseudo-nitzschia spp. Contrasting wind patterns, and their influence on water column structure and mesoscale circulation, led to predictably different assemblages of phytoplankton life-forms and their associated toxins.