During this study, we investigated the seasonal variability of the concentration and the stable isotope composition of several inorganic and organic matter reservoirs in the large, oligotrophic and deep tropical Lake Kivu (East Africa). Data were acquired during one year at a fornightly temporal resolution. The δ 13 C signature of the dissolved inorganic carbon (DIC) increased linearly with time during the rainy season, then suddenly decreased during the dry season due to vertical mixing with δ 13 C-depleted DIC waters. This pattern reflects the net autotrophic status of the mixed layer of Lake Kivu, contrary to the common observation that oligotrophic aquatic ecosystems tend to be net heterotrophic. The δ 13 C signature of the particulate organic carbon pool (POC) revealed the presence of a consistently abundant methanotrophic biomass in the oxycline throughout the year. We also noticed a seasonal shift during the dry season toward higher values in the δ 15 N of particulate nitrogen (PN) in the mixed layer and δ 15 N-PN was significantly related to the contribution of cyanobacteria to the phytoplankton assemblage, suggesting that rainy season conditions could be more favourable to atmospheric nitrogen-fixing cyanobacteria. Finally, zooplankton were slightly enriched in δ 13 C compared to the autochtonous POC pool, and the δ 15 N signature of zooplankton followed well the seasonal variability in δ 15 N-PN, being consistently 3.0 ± 1.1‰ heavier than the PN pool. Together, δ 13 C and δ 15 N analysis suggests that zooplankton directly incorporate algal-derived organic matter in their biomass, and they would rely almost exclusively on this source of organic matter throughout the year in general agreement with the very low allochthonous organic matter inputs from rivers in Lake Kivu.