We collected Arctic Ocean water column samples for methane (CH4) and nitrous oxide (N2O) analysis on three separate cruises in the summer and fall of 2015, covering a ∼10,000 km transect from the Bering Sea to Baffin Bay. This provided a three-dimensional view of CH4 and N2O distributions across contrasting hydrographic environments, from the oligotrophic waters of the deep Canada Basin and Baffin Bay, to the productive shelves of the Bering and Chukchi Seas. Percent saturation relative to atmospheric equilibrium ranged from 30 to 800% for CH4 and 75 to 145% for N2O, with the highest concentrations of both gases occurring in the northern Chukchi Sea. Nitrogen cycling in the shelf sediments of the Bering and Chukchi Seas likely constituted the major source of N2O to the water column, and the resulting high N2O concentrations were transported across the Arctic Ocean in eastward-flowing water masses. Methane concentrations were more spatially heterogeneous, reflecting a variety of localized inputs, including likely sources from sedimentary methanogenesis and sea ice processes. Unlike N2O, CH4 was rapidly consumed through microbial oxidation in the water column, as shown by the 13C enrichment of CH4 with decreasing concentrations. For both CH4 and N2O, sea-air fluxes were close to neutral, indicating that our sampling region was neither a major source nor sink of these gases. Our results provide insight into the factors controlling the distribution of CH4 and N2O in the North American Arctic Ocean, and an important baseline data set against which future changes can be assessed.