From 28 August to 6 September 1995, we monitored the lake-wide physical, chemical and biological properties of the pelagic waters in Lake Tanganyika. The aim of this study was to examine the spatial environmental variability and its relation to fluctuations in plankton abundance and community assembly. Trade winds had triggered an overall downward tilt of the isotherms; accumulation of warm surface waters and intensified stratification towards the north along with upwelling increased mixing, combined with decreased stratification towards the south. Dissolved oxygen, turbidity, conductivity, phosphorus and chlorophyll-a were higher; whereas temperature and pH were lower in southern than in northern waters. We observed a transition zone (6 to 7°S) where vertical water column structures changed from northern to southern conditions. This did not include the river Rusizi affected regions north of 4°S. High spatial heterogeneity in nutrient supply and degree of mixing had a strong impact on the plankton community. While the northern environments appeared to be based on reduced internal nutrient loading, lower phytoplankton biomass and smaller sized zooplankton with an important role of Cyclopoids, the mixed environments in the south seemed to be based on increased phosphorus availability and larger sized zooplankton dominated by Calanoid grazers. We emphasise that wind-driven formation of a gradual change in physical and chemical properties of the productive zones along the north-south axis of Lake Tanganyika is of importance in regionally determining nutrient flows. This consequently affects plankton community structures and composition, and therefore food web structure and functioning.