Inland waters were recently recognized to be important sources of methane (CH4) and carbon dioxide (CO2) to the atmosphere, and including inland water emissions in large scale greenhouse gas (GHG) budgets may potentially offset the estimated carbon sink in many areas. However, the lack of GHG flux measurements and well-defined inland water areas for extrapolation, make the magnitude of the potential offset unclear. This study presents coordinated flux measurements of CH4 and CO2 in multiple lakes, ponds, rivers, open wells, reservoirs, springs, and canals in India. All these inland water types, representative of common aquatic ecosystems in India, emitted substantial amounts of CH4 and a major fraction also emitted CO2. The total CH4 flux (including ebullition and diffusion) from all the 45 systems ranged from 0.01 to 52.1 mmol m−2 d−1, with a mean of 7.8 ± 12.7 (mean ± 1 SD) mmol m−2 d−1. The mean surface water CH4 concentration was 3.8 ± 14.5 μm (range 0.03–92.1 μm). The CO2 fluxes ranged from −28.2 to 262.4 mmol m−2 d−1 and the mean flux was 51.9 ± 71.1 mmol m−2 d−1. The mean partial pressure of CO2 was 2927 ± 3269 μatm (range: 400–11 467 μatm). Conservative extrapolation to whole India, considering the specific area of the different water types studied, yielded average emissions of 2.1 Tg CH4 yr−1 and 22.0 Tg CO2 yr−1 from India's inland waters. When expressed as CO2 equivalents, this amounts to 75 Tg CO2 equivalents yr−1 (53–98 Tg CO2 equivalents yr−1; ± 1 SD), with CH4 contributing 71%. Hence, average inland water GHG emissions, which were not previously considered, correspond to 42% (30–55%) of the estimated land carbon sink of India. Thereby this study illustrates the importance of considering inland water GHG exchange in large scale assessments.