Uncertainties in the magnitude and seasonality of various gas emission modes, particularly among different lake types, limit our ability to estimate methane (CH₄) and carbon dioxide (CO₂) emissions from northern lakes. Here we assessed the relationship between CH₄ and CO₂ emission modes in 40 lakes along a latitudinal transect in Alaska to lakes' physicochemical properties and geographic characteristics, including permafrost soil type surrounding lakes. Emission modes included direct ebullition, diffusion, storage flux, and a newly identified ice-bubble storage (IBS) flux. We found that all lakes were net sources of atmospheric CH₄ and CO₂, but the climate warming impact of lake CH₄ emissions was 2 times higher than that of CO₂. Ebullition and diffusion were the dominant modes of CH₄ and CO₂ emissions, respectively. IBS, ~10% of total annual CH₄ emissions, is the release to the atmosphere of seasonally ice-trapped bubbles when lake ice confining bubbles begins to melt in spring. IBS, which has not been explicitly accounted for in regional studies, increased the estimate of springtime emissions from our study lakes by 320%. Geographically, CH₄ emissions from stratified, mixotrophic interior Alaska thermokarst (thaw) lakes formed in icy, organic-rich yedoma permafrost soils were 6-fold higher than from non-yedoma lakes throughout the rest of Alaska. The relationship between CO₂ emissions and geographic parameters was weak, suggesting high variability among sources and sinks that regulate CO₂ emissions (e.g., catchment waters, pH equilibrium). Total CH₄ emission was correlated with concentrations of soluble reactive phosphorus and total nitrogen in lake water, Secchi depth, and lake area, with yedoma lakes having higher nutrient concentrations, shallower Secchi depth, and smaller lake areas. Our findings suggest that permafrost type plays important roles in determining CH₄ emissions from lakes by both supplying organic matter to methanogenesis directly from thawing permafrost and by enhancing nutrient availability to primary production, which can also fuel decomposition and methanogenesis.