Increasingly variable rainfall patterns expose soils to more frequent waterlogging in humid climates. Yet, the effects of waterlogging on soil organic matter decomposition in mineral soils remain uncertain. We studied the impact of off-season waterlogging on carbon dioxide (CO₂) and methane (CH₄) production, and dissolved carbon dynamics in controlled greenhouse conditions using 32 soil profiles (h=63 cm, d=15.2 cm) sampled from two agricultural fields (silty clay, sandy loam) in southern Finland. During the 1.5-year study comprising three growth cycles, spring barley (<em>Hordeum vulgare</em>) was grown during the growing seasons. During the off-seasons, half of the monoliths were subjected to waterlogging episodes of seven weeks, while in the control monoliths soil moisture was maintained below field capacity. Additionally, overwintering cover crop (<em>Festuca arundinacea</em>) was grown in half of the monoliths. Soil temperature and moisture were continuously monitored, dissolved organic (DOC) and inorganic carbon (DIC) concentrations in pore water were analyzed at three depths, and CO₂ and CH₄ fluxes were measured at the surface. Temporary waterlogging did not induce CH₄ production in either soil. Contrary to our hypothesis, waterlogging did not increase soil DOC content. Instead, on-going microbial/rhizospheric activity promoted an increase in DIC content while CO₂ fluxes declined, indicating an accumulation of respired CO₂in soil pore water. This sustained CO₂ production could not be explained solely by mobilization of Fe-associated C, as initially hypothesized. After the initiation of drainage, CO₂ fluxes from both soils and plant treatments increased more than predicted based on changes in soil moisture and temperature, likely due to the release of previously accumulated CO₂. These post-waterlogging increases in CO₂ fluxes roughly equaled the earlier decreases during waterlogging. Thus, although off-season waterlogging strongly influenced the temporal dynamics of CO₂ fluxes, it did not alter total cumulative CO₂ emissions from the studied agricultural soils.