Boreal inland waters are hotspots for greenhouse gas emissions, and they play an important role in quantifying the regional carbon budget, but seasonal variations in their emissions are not well understood. In this study, we observed the concentration of carbon dioxide (CO₂) and methane (CH₄) trapped in the ice during the ice cover period of the Fukuchi River and its diverted oxbow lakes (late successional stage) in the permafrost zone of the Great Hing'an Mountains. Differences in dissolved CO₂ and CH₄ concentrations in the two water bodies during three periods (ice cover period, open water period, and spring thaw period) were also compared. The results showed that there were differences in the seasonal variation patterns of dissolved CO₂ and CH₄ concentrations in the two water bodies. Concentrations of dissolved CO₂ and CH₄ were highest in the water column of oxbow lakes during the ice cover period. There was a significant accumulation of CO₂ and CH₄ under the ice layer. The mean dissolved CH₄ concentration in the water column was (2.21±0.54) μmo/L, which was 5 and 14 times higher than the CH₄ concentration during the open water and spring thaw periods, respectively. River had the highest dissolved CO₂ and CH₄ concentrations in the water column during the spring thaw period, which were significantly higher than during the open water period and ice cover period (P<0.05). Dissolved CO₂ and CH₄ in water were influenced by various environmental factors and were positively correlated with dissolved organic carbon (DOC) (P<0.05) and negatively correlated with dissolved oxygen (DO) and water temperature (P<0.05). CO₂ and CH₄ were also trapped within the ice as bubbles when the ice formed during the ice cover period. CO₂ was the main component in bubbles, with concentrations of about 90% or more within the bubbles. As CO₂ and CH₄ concentrations in bubbles are about 1%-30% of those in the water column under the ice, ignoring the greenhouse gases stored in the ice would increase the uncertainty of carbon emissions from boreal inland waters. This study clarified the seasonal characteristics of dissolved CO₂ and CH₄ and the winter storage capacity of two water bodies in the Great Hing'an Mountains permafrost region. The results provide important data to understand carbon cycling processes in the water bodies of this region.