Lake Kivu is one of the large African Rift lakes situated between the Democratic Republic of the Congo and Rwanda. In its permanently stratified hypolimnion, unusually high methane concentrations have increased further in recent decades. Because methanogenesis is, in part, dependent on supply of organic material from the photic zone, it is necessary to quantify upward nutrient fluxes from the saline, nutrient-rich deep waters. These upward fluxes are mainly driven by advection caused by subaquatic springs. Biogenic calcite precipitation drives surface-water depletion and deep-water enrichment of Ca(2+), Sr(2+), and Ba(2+). Methane is mainly oxidized aerobically at the redox interface at 60 m, with a small contribution of anaerobic methane oxidation. A subaquatic spring that sustains the major chemocline at 250 m depth was depleted of N, P, and CH(4), and concentrations of major ions were slightly lower than in the lake water of the same depth. Enrichment of the deep waters with nutrients and CH(4) are driven by mineralization of settling organic material, whereas SiO(2) is influenced by uptake and mineralization of diatoms and inputs through subaquatic springs. Dissolved inorganic phosphorus and Si fluxes supplied by internal loading through upwelling were found to be lower than the estimations for Lakes Malawi and Tanganyika. In contrast, N flux was within the lower range for Lake Malawi, whereas it was assumed to be totally lost by denitrification in Lake Tanganyika. In Lake Kivu, nutrient uptake by primary production is three times higher than nutrient upward fluxes.