This dataset provides estimates of carbon dioxide (CO2) and methane (CH4) diffusive fluxes from waterbodies, and watershed landcover data for the central-interior of the Yukon-Kuskokwim Delta (YK delta), Alaska. Dissolved concentrations of methane and carbon dioxide were predicted using an integrated terrestrial-aquatic approach to scale observations based on landscape and waterbody remote sensing drivers. The observations include ~300 samples of surface water dissolved gases collected in July 2016-2019 from the central region of the YK Delta, Alaska. A machine learning model was used to generate estimated fluxes. Model inputs include Sentinel-2 MSI with derived normalized difference vegetation index (NDVI) and normalized difference water index (NDWI), an Arctic digital elevation model (DEM) with derived slope and flow accumulation, Sentinel-1 C-band July and December VV and VH composites, and a landcover map. Waterbody size, shape, and reflectance were determined using object-based image analysis in Google Earth Engine. Landscape-level input data were averaged in non-nested sub-basins calculated using the System for Automated Geoscientific Analyses (SAGA) "channel network" algorithm at three threshold sizes. Cross validation was used to tune and select variables for gradient boosting models. The trained gradient boosting models were then used to predict dissolved methane and carbon dioxide in all waterbodies (~17,000) in the region. These aquatic concentrations were converted to fluxes using an average gas transfer velocity from observations (0.33 m/d). The data are provided in GeoTIFF and shapefile formats.