Numerous rivers and lakes in the monsoon climate zone are heavily influenced by frequent rainstorms that mobilize dissolved organic matter (DOM) from pristine or urbanized environments into downstream lakes. Of particular concern is the mobilization of DOM from anthropogenic effluents, which are commonly enriched in aliphatic compounds that can be easily degraded by microorganisms. Rapid degradation of highly biodegradable DOM, in turn, may cause significant depletion of dissolved oxygen in the water, which, by creating anoxic conditions at the bottom water-sediment interface, promotes microbial production of CO2 and CH4. Further investigations based on high-frequency monitoring and novel techniques such as ultrahigh-resolution mass spectrometry and isotopic measurements, are needed to elucidate the processes and mechanisms by which pulsed aliphatic inputs impact lake carbon emissions.