<p>Rice paddies are substantial sources of methane emissions, with CH₄ released into the atmosphere through three pathways: molecular diffusion of dissolved methane across the atmosphere-water boundary, ebullition of gas bubbles, and diffusive transport through the aerenchyma tissue of rice plants. This study aimed to analyze seasonal variations in CH₄ fluxes separately via ebullition and rice plants and to explore the potential relation between in situ gas volume and CH₄ emissions. Field monitoring of CH₄ emissions, gas-filled porosity (that is, bubble volume), and soil temperature was conducted in a rice paddy with four different treatments: plots with/without rice plants (<i>Oryza sativa</i> ‘Koshihikari’) and with/without straw application. Results indicated that both total CH₄ flux and CH₄ ebullition were higher during the ripening stage for plots without straw application, and over 60% of total CH₄ flux was attributed to ebullition. Rice straw application enhanced both fluxes during the early vegetative stages. Seasonal trends in the total CH₄ flux corresponded to those of the CH₄ flux via ebullition. Gas-filled porosity increased during the vegetative stage, particularly in plots with straw application, reaching maximum values during the late reproductive stage. The methane flux via rice plants and ebullition correlated well with gas-filled porosity during the vegetative and reproductive stages. This study suggests that the size of the gaseous CH₄ pool is a good measure for estimating the flux intensities of both the ebullition- and rice-mediated pathways.</p>