Arctic river deltas and deltaic near-shore zones represent important land-ocean transition zones influencing sediment dynamics and nutrient fluxes from permafrost-affected terrestrial ecosystems into the coastal Arctic Ocean. To accurately model fluvial carbon and freshwater export from rapidly changing river catchments, as well assessing impacts of future change on the Arctic shelf and coastal ecosystems, we need to understand the sea floor characteristics and topographic variety of the coastal zones. To date, digital bathymetrical data from the poorly accessible, shallow and large areas of the eastern Siberian Arctic shelves are sparse. We have digitized bathymetrical information for nearly 75,000 locations from large-scale (1:25,000 – 1:500,000) current and historical nautical maps of the Lena Delta and the Kolyma Gulf region in Northeast Siberia. We present the first detailed and seamless digital models of coastal zone bathymetry for both delta/gulf regions in 50 m and 200 m spatial resolution. We validated the resulting bathymetry layers using a combination of our own water depth measurements and a collection of available depth measurements, which showed a strong correlation (r > 0.9). Our bathymetrical models will serve as an input for a high-resolution coupled hydrodynamic-ecosystem model to better quantify fluvial and coastal carbon fluxes to the Arctic Ocean but may be useful for a range of other studies related to Arctic delta and near-shore dynamics such as modelling of submarine permafrost, near-shore sea ice, or shelf sediment transport.