The productive but highly exposed coastline of the southern Benguela eastern boundary upwelling system offers limited natural environment for aquaculture. Saldanha Bay located on the west coast of South Africa is one of the few embayments on the coastline that provides a productive and relatively sheltered environment suitable for the cultivation of shellfish. Consequently, bivalve culture in South Africa is centered in Saldanha Bay and is presently targeted for expansion. Pseudo-nitzschia blooms including toxin-producing species are shown to contribute significantly to the phytoplankton of Saldanha Bay specifically in spring and summer. Their dominance at this time of the year, when upwelling is strongest, fits the ecological profile of Pseudo-nitzschia occurring during periods of high turbulence and nutrients. Multiple Pseudo-nitzschia blooms were sampled under varying environmental conditions and the strength of the relationship between Pseudo-nitzschia cell abundance and particulate domoic acid (pDA) content, reflecting bloom toxicity, varied greatly. This variability is the result of the combined influence of species and strain composition of the Pseudo-nitzschia assemblage and the effect of environmental conditions on toxin production. Elevated levels of pDA were associated with higher concentrations of cells of the P. seriata complex differentiated by frustule width (>3 µm). P. australis was identified as a toxin-producing species and a prominent member of the P. seriata complex. Low DA levels in shellfish in Saldanha Bay are considered a function of low cellular domoic acid (cDA). Silicate limitation has emerged as an important factor inducing DA production in Pseudo-nitzschia species. The high ratio of silicate to nitrate in Saldanha Bay provides a plausible explanation for the low toxin content of Pseudo-nitzschia blooms in the bay and the consequent low risk posed by these blooms to the aquaculture sector.