We are among the first to quantify methane emissions from inland water system in the pan-Arctic. The total CH₄ emissions are 36.46 Tg CH₄ yr⁻¹ during 2000–2015, of which wetlands and lakes were 21.69 Tg yr⁻¹ and 14.76 Tg yr⁻¹, respectively. By using two non-overlap area change datasets with land and lake models, our simulation avoids small lakes being counted twice as both lake and wetland, and it narrows the gap between two different methods used to quantify regional CH₄ emissions.