Non-marine waters (i.e., rivers, reservoirs, lakes, ponds, streams and estuaries) are globally significant emitters of methane (CH4) and nitrous oxide (N2O) to the atmosphere, while global estimates of these emissions have been hampered due to the lack of a worldwide comprehensive database with the collection of complete CH4 and N2O flux components. Here we synthesize 2997 in-situ flux or concentration measurements of CH4 and N2O from 277 peer-reviewed publications to examine the role of non-marine waters in shaping climate change. Here we estimate that inland waters including rivers, reservoirs, lakes and streams together release 94.49 Tg CH4 yr− 1 (ebullition plus diffusion) and 1.52 Tg N2O yr− 1 (diffusion) to the atmosphere, yielding an overall CO2-equivalent emission total of 3.05 Pg CO2 yr− 1, representing roughly 59% of CO2 emissions (5.13 Pg CO2 yr− 1) from these four aquatic ecosystems, with lakes acting as the largest emitter for both trace gases. Ebullition is noticed as a dominant flux component, contributing up to 62–84% of total CH4 fluxes across all inland waters. Chamber-derived CH4 flux rates are significantly greater than those determined by diffusion model-based methods for commonly capturing of both diffusive and ebullitive fluxes. The synthesis of global N2O measurements projected that rivers exhibit the highest indirect N2O emission factor (EF5, 0.028%), while streams have the lowest EF5 value (0.015%). Our study reveals a major oversight in regional and global CH4 budgets from inland waters, caused by neglect of the dominant role of ebullition pathways in those emissions. The indirect EF5 values established in this study generally suggest an order of magnitude downward revision is required in current IPCC default EF5 values for inland waters and estuaries. Our findings further indicate that a comprehensive understanding of the magnitude and patterns of CH4 and N2O emissions from non-marine waters is essential in defining the way that these natural ecosystems shape our climate.