In southern Lake Malawi, seasonal pelagic chlorophyll means were 1.0 ± 0.3 μg L⁻¹ in the deep mixing season (DMS) (May–August), 0.8 ± 0.3 μg L⁻¹ in the dry stratified season (DSS) (September to November) and 0.7 ± 0.3 μg L⁻¹ in the wet stratified season (WSS) (December to April). Despite the low variability in chlorophyll, there was a wide range in chlorophyll specific photosynthetic activity. The photosynthetic parameters, P^b_m (the light saturated rate) and α^b (the light limited slope), varied significantly among seasons and were highly positively correlated, with lowest values in the DSS and highest values in WSS. During deep mixing, P^b_m did not covary with α^b; and the light saturation index, E_k (=Pb_m/α^b), varied in response to changes in α^b rather than in P^b_m. Phytoplankton appeared to be nutrient deficient at all times but less deficient during deep vertical mixing in the DMS. Average daily rates of integrated phytoplankton primary productivity were lowest in the DSS (337 mg C m⁻² d⁻¹) and highest in the WSS (629 mg C m⁻² d⁻¹) despite nearly identical mean chlorophyll concentrations. Along a near shore transect off the Linthipe River, chlorophyll concentrations were higher and more variable (1.4 ± 1.3 μg L⁻¹), phytoplankton were not strongly nutrient deficient and chlorophyll specific photosynthetic activity was as high or higher than at the offshore station. Estimates of phytoplankton productivity in this tropical great lake must account for spatial and temporal variability in photosynthetic parameters imposed by seasonal changes in mixing dynamics.