Characterizing the processes which cause upwelling in the East African Great Lakes enables prediction of the spatial–temporal variability of phytoplankton blooms and increases in fish abundance or incidence of fish kills. The influence of the southeast trade winds on the limnology of Lake Tanganyika is well known. Upwelling occurs to the south and downwelling to the north from May to September and subsequent upwelling and blooms at the northern end of the lake. However, the influence of the shifts in wind speed and direction after the SE trade winds, including the Northeast trade winds, and any further internal wave driven upwelling requires investigation. Here we use images from remote-sensing during a 12 year period (2003–2014) to illustrate intense phytoplankton blooms at the southeast of Lake Tanganyika in April-May, a period characterized by relaxation of the Northeast trade winds. Phytoplankton blooms progressed around the lake after a massive cyanobacteria bloom at the northern end in September 2018; recent and historical observations and local knowledge show similar patterns. Lake Tanganyika limnological cycle is revised to include four main periods: two trade winds seasons and two inter-monsoon seasons (April-May and September-October) with lake-wide up and downwelling of the thermocline associated with the monsoons, and upwelling associated with subsequent internal waves in the inter-monsoon period which are linked with increased phytoplankton blooms and sometimes also fish kills.