Previous studies typically assumed a constant total organic carbon (OC) storage in the lake water column, neglecting its significant variability within a changing world. Based on extensive field data and satellite monitoring techniques, we demonstrate considerable spatiotemporal variability in OC concentration and storage for 24,366 Chinese lakes during 1984–2023. Here we show that dissolved OC concentration is high in northwest saline lakes and particulate OC concentration is high in southeast eutrophic lakes. Along with increasing OC concentration and water volume, dissolved and particulate OC storage increase by 44.6% and 33.5%, respectively. Intensified human activities, water input, and wind disturbance are the key drivers for increasing OC storage. Moreover, higher OC storage further leads to an 11.0% increase in nationwide OC burial and a decrease in carbon emissions from 71.1% of northwest lakes. Similar changes are occurring globally, which suggests that lakes are playing an increasingly important role in carbon sequestration.