In this study, an analytical model for the transport of biofilm-coated sediment (bio-sediment) particles is developed. Experiments were conducted cultivating biofilm-coat around fine sediment particles (silt type) in an experimental flume for a specific period of time. The particle tracking velocimetry method was used to detect the saltation trajectory, the size of bio-flocs, and the flow velocity. A concentration meter was used to measure the concentrations of near-bed and suspended sediment transport. It was observed that the ratio of saltation length to saltation height for bio-flocs is greater than that for uncontaminated (without a biofilm-coat) sediment particles. The experimental data were used to calibrate the analytical model. A relationship for the bed-load transport rate of bio-sediments as a function of transport stage and particle parameters is proposed. Also, a formula for the reference concentration is given. Then, a computational scheme of bio-sediment transport (both bed-load and suspended-load transport) is furnished. © 2016 International Association for Hydro-Environment Engineering and Research.