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Western Siberia contains extensive wetlands and aquatic ecosystems, contributing a significant amount of methane (CH4) emissions to the atmosphere. However, estimates of CH4 fluxes over the region are poorly constrained partly due to the uncertainties from the inundated area data. This study applied two process‐based biogeochemistry models to quantify the emissions from land and aquatic ecosystems over the region within the period 2000–2021 using different inundation datasets. To drive land methane modeling, we use one static wetland map and one dynamic wetland area data set called Wetland Area and Dynamics for Methane Modeling (WAD2M) (2000–2020). To drive lake methane modeling, we use the surface area of aquatic ecosystems from three datasets: (a) HydroLAKES; (b) Global Surface Water (GSW); and (c) surface water inundation from Soil Moisture Active Passive (SMAP) (2016–2021). Using these datasets, we conduct four simulations to compare emissions over the region. We find that the net methane emissions from land using the static wetland map are larger than those using WAD2M. SMAP and GSW estimate larger emissions than HydroLAKES does from aquatic ecosystems. Total emissions over the region range from 4.80 ± 0.43 to 8.29 ± 0.81 Tg CH4/year from 2016 to 2020, which is the intersection period of four simulations. This study is among the first to investigate methane emissions from the whole landscape in the region. Our study highlights the importance of dynamic wetland and aquatic area data in quantifying regional methane emissions. Plain Language Summary: Methane (CH4) is a vital greenhouse gas that can make large differences in global climate change. In this study, we quantified total methane emissions over Western Siberia, which is a methane‐emitting hotpot. We used two process‐based models to quantify methane emissions from both land and aquatic ecosystems over the region. We used different combinations of wetlands and aquatic areal datasets to run four model simulations for comparison. We found that the total emissions over the region range from 4.80 ± 0.43 to 8.29 ± 0.81 Tg CH4/year from 2016 to 2020 depending on the land and aquatic areal dynamics. We conclude that it is important to develop dynamic wetland and aquatic area data in quantifying regional methane emissions. Key Points: Methane emissions from both land and aquatic ecosystems over Western Siberia are quantifiedTotal methane emissions over Western Siberia range from 4.80 ± 0.43 to 8.29 ± 0.81 Tg CH4/year from 2016 to 2020It is important to develop both dynamic wetland and aquatic area data in quantifying regional methane emissions [ABSTRACT FROM AUTHOR]