In this study, we analyze the circulation patterns in Lake Tanganyika, a large, economically important water body in East and Central Africa, which has experienced significant warming in recent decades. Using the Regional Ocean Modeling System (ROMS) model with a 2.1 km resolution grid and 16 vertical layers, we examine thermal stratification, wind-driven processes, and circulation dynamics. Our results show seasonal variations in surface water temperature caused by changes in air temperature and wind conditions. Primary upwelling occurs in the southern regions from May to August, while secondary upwelling is seen in the northern areas from November to February consistent with previous instrumental studies. Bathymetry affects both upwelling and downwelling circulation. Our findings highlight the interplay between atmospheric and hydrodynamic factors controlling nutrient distribution within the lake driven by internal circulation. These insights underscore the importance of continuous monitoring and collaborative management to protect Lake Tanganyika’s ecosystem amid climate change.