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(Sub)tropical inland waters are important greenhouse gas (GHG) sources, yet limited observations have long hindered broad analyses of GHG variability across this diverse region. Here, through a meta-analysis, we have examined the rates and drivers of GHG emissions from flowing and standing (sub)tropical inland waters. We find considerable spatial variation in fluxes, largely related to differences in hydroclimate, geomorphology, land cover and human disturbance. Flowing waters emit more carbon dioxide (3,3872,1215,702 TgCO2 yr−1, expressing medianfirst quartilethird quartile), methane (10.60.128.8 TgCH4 yr−1) and nitrous oxide (0.620.351.10 TgN2O yr−1) than standing waters (11473219 TgCO2 yr−1, 5.42.19.1 TgCH4 yr−1 and 0.030.020.05 TgN2O yr−1, respectively). (Sub)tropical inland waters release 4,23824737375 TgCO2-equivalents annually, with first- to third-order streams contributing 75% of riverine emissions and lakes larger than 100 km2 contributing 59% of standing water emissions. Our results suggest emissions from (sub)tropical waters are 29–72% lower than earlier estimates, a downward revision with important implications for global GHG budgets.