Lake Kivu is a 485 m deep tropical rift lake in East-Africa and well-known for its very high concentrations of dissolved carbon dioxide and methane in the stratified deep waters. In view of future large-scale methane extraction for power production, there is a need for predicting the evolution of gas concentrations and lake stability using numerical modelling. However, knowledge about the geochemical origin and transport processes affecting dissolved gases in the lake is still partially missing. Due to their inert nature, the analysis of dissolved noble gases can help to shed light on such questions. To learn more about transport processes in Lake Kivu, we extended a well-established sampling method for dissolved noble gases to work in the lake's high gas pressure waters. The results of our analysis show a distinct non-atmospheric isotopic signal in the deep waters (below 250 m) with 3He/4He and 40Ar/36Ar ratios ~250% and ~20% higher than air saturated water (ASW). Moreover, the gas concentration profiles reveal a striking lack of atmospheric noble gases in the deep waters with respect to ASW. While Ne is depleted by ~45%, the more soluble 36Ar and Kr even decrease by ~70%. In contrast, 4He concentrations increase with depth by a factor of up to ~600. We attribute this excess He and the increases in 3He/4He and 40Ar/36Ar to the inflow of magmatic gases into Lake Kivu, along with a significant contribution of radiogenic 4He. To explain the depletion of atmospheric noble gases, we present and discuss three different scenarios, namely continuous outgassing, the inflow of depleted groundwater and a large past outgassing event. Due to the best agreement with our observations, we conclude that the inflow of depleted groundwater is likely responsible for the observed atmospheric noble gas depletions.