Peatland catchments store vast amounts of carbon. Humic lakes and pools are the primary receptacles for terrigenous carbon in these meta-ecosystems, representing sequestration hotspots; boreal lakes alone store ca. 120 Pg C. But little is known about the mechanisms that preserve aquatic carbon stocks. Here, we determined the regulatory pathway of decomposition in relation to ‘traditional’ limitations, namely anoxia, decay inhibiting compounds, low nutrients and acidity, using in vitro manipulation, mesocosms and natural gradients. We show that anoxia represents a powerful hierarchical preservation mechanism affecting all major limitations on decomposition and recapturing carbon that would otherwise escape from peatlands. Oxygen constraints on microbial synthesis of oxidases and nutrient-cycling enzymes, prevents the decay of organic matter to CO2, CH4 and N2O by allowing inhibitor accumulation and lowering nutrients. However, this pathway is sensitive to direct nutrient inputs and therefore eutrophication could initiate catastrophic feedback to global warming via dramatically increased greenhouse gas emissions. Identifying these process-specific limitations should inform better management and conservation of these vital systems.