Abstract: The mass exchange across sediment-water interface for rough bed depends on not only the hydrodynamic condition, but also the physical feature of the sediment bed and the bedform configuration. To take the comprehensive impact of sediment permeability and microtopography for the rough bed on the mass exchange process across the sediment-water interface into account, quantitative data and variation characteristics of interfacial mass exchange flux and effective diffusion coefficient under different conditions of the sandy beds without and with discrete roughness elements have been measured and obtained by means of laboratory annular flume experiment. A parameterization method has been adopted to analyze the dominant mechanism of interfacial mass exchange within the variation range of non-dimensional controlling parameters. The experimental results indicate that the sediment permeability and microtopography of the rough bed play a key role in the interfacial mass exchange process. An additional bumping exchange driven by the local flow structure around each roughness element increases interfacial mass exchange flux to varying degrees as compared to that for the case of flat bed, and this enhancement effect is closely related to the variations of the sediment permeability and bed roughness. The effective diffusion coefficient tends to increase on the whole with the increasing sediment permeability and bed roughness. Turbulence penetration shows an enhanced effect on the interfacial mass exchange, and the relative importance of the bumping exchange shows an attenuated effect trend. Therefore, an analysis of the dominant interfacial mass exchange mechanism for the rough bed with microtopography should take the comprehensive impact of the sediment permeability and bed roughness into consideration.