Lake deoxygenation is of growing concern because it threatens ecosystem services delivery. Complete deoxygenation, anoxia, is projected to prolong and expand in lakes, promoting the production or release of nutrients, greenhouse gases and metals from the water column and sediments. Accumulation of these compounds cannot be easily predicted thus hindering our capacity to forecast the ecological consequences of global changes on aquatic ecosystems. Here, we used monitoring data of four lakes to develop a novel tool, anaerobic duration, to study anaerobic processes in lake waters. Anaerobic duration explained, as a single predictor, 21–60% of the variation for ammonium, phosphorus and a dissolved organic matter fluorophore. Anaerobic duration could be modeled using only two oxygen profiles and lake bathymetry, making it an easily applicable tool to interpret and extrapolate biogeochemical data. This novel tool thus has the potential to transform widely available oxygen profiles into an ecologically meaningful variable.