Rice and the distinctive cultivation practices employed in rice growth can significantly influence the environmental fate of polybrominated diphenyl ethers (PBDEs) in a paddy field. We studied variations in PBDE concentrations in multiple compartments of a paddy field in the suburban area of Guangzhou, South China, including air, soil, water, and rice tissues. The input/output fluxes of air–surface and air–foliage exchange, atmospheric deposition and water input during different rice growth stages were measured simultaneously. Air–foliage and air–water diffusion exchanges were the key processes controlling inputs and outputs of PBDEs in paddy fields, respectively, whereas atmospheric deposition dominated inputs of higher brominated PBDEs. The high input of PBDEs via air–foliage exchange suggested that vegetation can significantly increase the air-to-field transport of PBDEs in ecosystems. The annual input of PBDEs in all paddy fields in Guangdong Province was estimated to be 22.1 kg.