During this study, we investigated the seasonal variability of the concentration and the stable isotope composition of several inorganic and organic matter (OM) reservoirs in the large, oligotrophic and deep tropical Lake Kivu (East Africa). Data were acquired over 1 year at a fortnightly temporal resolution. The δ¹³C 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 ¹³C-depleted DIC waters. The δ¹³C 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 δ¹⁵N of particulate nitrogen (PN) in the mixed layer and δ¹⁵N-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 ¹³C compared to the autochthonous POC pool, and the δ¹⁵N signature of zooplankton followed well the seasonal variability in δ¹⁵N-PN, consistently 3.0 ± 1.1 ‰ heavier than the PN pool. Together, δ¹³C and δ¹⁵N analysis suggests that zooplankton directly incorporate algal-derived OM in their biomass, and that they rely almost exclusively on this source of OM throughout the year in general agreement with the very low allochthonous OM inputs from rivers in Lake Kivu.