China’s lakes shifted from a CO2 source to a sink over two decades

China’s lakes are globally significant and have experienced widespread changes, however, how they shift their roles in CO2 emissions over time remains elusive due to a shortage of time series data. We took advantage of two national lakes surveys to calculate the CO2 partial pressure (pCO2) and quantify the CO2 emissions during two time periods (1988-1992 and 2007-2010). Lakes across China have shifted from a substantial CO2 source (2.748 Tg C yr-1) to a minor sink (-0.408 Tg C yr-1), advocated by the fact that pCO2 was halved from 709 μatm to 332 μatm. This shift was predominantly caused by increased primary production in eutrophic lakes, decreased external loadings in organic carbon-rich lakes, and expanded water volume in endorheic lakes. This nationwide CO2 source-sink transition highlighted the roles of multiple mechanisms in altering CO2 flux in lakes, calling for a comprehensive investigation of multiple environmental changes in assessing CO2 dynamics.