Arctic and boreal lake greenhouse gas emissions (GHG) are an important component of regional carbon (C) budgets. Yet the magnitude and seasonal patterns of lake GHG emissions are poorly constrained, because sampling is limited in these remote landscapes, particularly during winter and shoulder seasons. To better define patterns of under ice GHG content (and emissions potential at spring thaw), we surveyed carbon dioxide (CO2) and methane (CH4) concentrations and stable isotopic composition during winter of 2017 in 13 lakes in the arid Yukon Flats Basin of interior Alaska, USA. Partial pressures of CO2 and CH4 ranged over three orders of magnitude, were positively correlated, and CO2 exceeded CH4 at all but one site. Shallow, organic matter-rich lakes located at lower elevations tended to have the highest concentrations of both gases, though CH4 content was more heterogeneous and only abundant in oxygen-depleted lakes, while CO2 was negatively correlated to oxygen content. Isotopic values of CO2 spanned a narrow range (−10‰ to −23‰) compared to CH4, which ranged over 50‰ (−19‰ to −71‰), indicating CH4 source pathways and sink strength varied widely between lakes. Miller-Tans and Keeling plots qualitatively suggested two groups of lakes were present; one with isotopically enriched source CH4 possibly more dominated by acetoclastic methanogenesis, and one with depleted signatures suggesting a dominance of the hydrogenotrophic production. Overall, regional lake differences in winter under ice GHG content appear to track landscape position, oxygen, and organic matter content and composition, causing patterns to vary widely even within a relatively small geographic area of interior Alaska.