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Floating vegetation islands (FVIs) have been widely utilized in various river ecological restoration projects due to their ability to purify pollutants. FVIs float at the surface of shallow pools with their roots unanchored in the sediment. Biofilm formed by roots under islands filters nutrients and particles in the water flowing through it. Flow field disturbance will occur and transverse distribution of flow velocity will change due to the existence of FVIs. Transport efficiency of suspended solids, nutrients, and pollutants will also be altered. A modified analytical model that considers effects of boundary friction, drag force of vegetation, transverse shear turbulence, and secondary flow is established to predict transverse variation of depth-averaged streamwise velocity for the open-channel flow with FVIs using Shiono and Knight method. The simulation results with suitable boundary conditions successfully predicted lateral profile of the depth-averaged streamwise velocity compared with the experimental results of symmetrical and unsymmetrical arrangements of FVIs. Hence, the presented model can provide guidance for investigating flow characteristics of rivers with FVIs.