A fully mechanistic model based on diffusion equations for gas transport in a flooded rice system is presented. The model has transport descriptions for various compartments in the water-saturated soil and within the plant. Plant parameters were estimated from published data and experiments independent of the validation experiment. An independent experiment is described in which the diffusion coefficient of sulfurhexafluoride (SF6) in water-saturated soil was determined. The model was validated by experiments in which transport of SF6 through soil and plant was monitored continuously by photoacoustics. The independent default settings could reasonably predict gas release dynamics in the soil-plant system. Calculated transmissivities and concentration gradients at the default settings show that transport within the soil was the most limiting step in this system, which explains why most gases are released via plant-mediated transport. The root-shoot interface represents the major resistance for gas transport within the plant. A sensitivity analysis of the model showed that gas transport in such a system is highly sensitive to the estimation of the diffusion coefficient of SF6, which helps to understand diel patterns found for greenhouse gas emissions, and to the root distribution with depth. This can be understood from the calculated transmissivities. The model is less sensitive to changes in the resistance at the root-shoot interface and in the root fraction active in gas exchange. The model thus provides an understanding of limiting steps in gas transport, but quantitative predictions of in situ gas transport rates will be difficult given the plasticity of root distribution.