Numerous studies have documented CO 2 dynamics in temperate lakes, but few such studies have been conducted on tropical lakes. Spatial and seasonal variation of air and water pCO 2 , along with supporting limnological and meteorological variables, were measured aboard a vessel of opportunity along the north-south axis of Lake Malawi. These measurements were used to estimate annual net lake-atmosphere CO 2 flux and infer mechanisms regulating it. Surface pCO 2 and CO 2 flux varied significantly with season and location. Temporally, the lake was CO 2 -undersaturated during the rainy season and the mixing season, and supersaturated at the onset of the mixing season and during the hot, stratified season. Concurrent measurements of lake temperature, weather conditions, phytoplankton biomass, and seston δ 13 C suggest that periods of net CO 2 flux into the lake correspond with higher phytoplankton growth rates resulting from internal nutrient loading in the mixing season and allochthonous nutrient inputs in the rainy season. Unlike the rest of the lake, the southernmost region of the lake was usually CO 2 supersaturated even though phytoplankton productivity is highest in this region. While the upwelling of hypolimnetic water at the southern end of the lake is a major source of nutrients that drive phytoplankton photosynthesis and CO 2 uptake, the CO 2 introduced in upwelled water appears to overwhelm photosynthetic capacity locally, especially at the onset of the mixing season. Lake Malawi appears to be a net CO 2 sink with an annual whole-lake CO 2 flux of −2.17 AE 0.25 × 10 10 mol C yr −1 and a mean daily CO 2 flux of −2.05 AE 0.27 mmol C m −2 d −1 . A comparison of deep-water C : P ratios with epilimnetic seston C : P ratios suggests that P is recycled more efficiently than C in the lake's anoxic hypolimnion, and so P vertical mixing creates a carbon deficit that is met by flux from the atmosphere into the lake.