Lake Tanganyika, the second largest freshwater ecosystem in Africa, is characterised by a significant heterogeneity in phytoplankton concentration linked to its particular hydrodynamics. To gather a proper understanding of primary production, it is necessary to consider spatial and temporal dynamics throughout the lake. In the present work, daily MODIS-AQUA satellite measurements were used to estimate chlorophyll-a concentrations and the diffuse attenuation coefficient (K490) for surface waters. The spatial regionalisation of Lake Tanganyika, based on Empirical Orthogonal Functions of the chlorophyll-a dataset (July 2002–November 2005), allowed for the separation of the lake in 11 spatially coherent and co-varying regions, with 2 delocalised coastal regions. Temporal patterns of chlorophyll-a showed significant differences between regions. Estimation of the daily primary production in each region indicates that the dry season is more productive than the wet season in all regions with few exceptions. Whole-lake daily primary productivity calculated on an annual basis (2003) was 646 ± 142 mg C m− 2 day− 1. Comparing our estimation to previous studies, photosynthetic production in Lake Tanganyika appears to be presently lower (about 15%), which is consistent with other studies which used phytoplankton biovolume and changes of δ13C in the lake sediments. The decrease in lake productivity in recent decades may be associated to changes in climate conditions.