This study presents a novel concept for estimating net ecosystem production (NEP), the export of organic carbon (OC) from the productive surface layer to the deep‐water (hypolimnion) of eleven seasonally stratified lakes, varying in depth and trophic state. As oxygen remineralizes settling OC at a constant ratio, NEP is equivalent to the areal hypolimnetic mineralization rate (AHM) plus burial in the sediment. Two major interferences have to be considered, however. First, OC from terrestrial sources, not originating from primary production, consumes a fraction of oxidants. Second, sediment diagenetic processes of lakes in trophic transition (e.g. undergoing eutrophication or reoligotrophication) that are not in quasi‐steady‐state with actual fluxes of OC from the productive surface layer, bias the NEP estimation. In these cases, the flux of reduced substances diffusing from the sediment must be subtracted. This results in some overestimation for lakes with high allochthonous loads, and slight underestimation in lakes that are not in quasi‐steady‐state, because the actual sediment burial of autochthonous OC is small but not negligible. The presented approach requires data from routinely available monitoring and thus can be applied to historic data. The temporal integration over the productive season makes the estimation of NEP robust. Based on a historic 47 years long data record of Lake Geneva, NEP estimations (∼70 gC m‐2) from AHM rates agree well with P and N export budgets from the productive surface zone, which help to verify and constrain the uncertainty of the estimates.