Unsteady flows are investigated in a compound open-channel flume, consisting of a Main Channel (MC) and an adjacent Flood Plain (FP). Two types of inflow hydrographs are studied, i.e., a discharge hydrograph with, at any time: a slightly unbalanced inflow partition between MC and FP (Case I); and a noticeably unbalanced inflow partition (Case II). Ensemble averages of the time-varying discharges, water depths and velocities are estimated based on 100 successive runs. The main focus of the experimental study is on assessing (i) the time-varying lateral discharge and depth-averaged Reynolds stress at the MC/FP interface, and (ii) the influence of the inflow partition on the downstream flow parameters. The experimental flows are then simulated using a 1D (one-dimensional) code that was adapted to implement the 1D+ Independent Sub-sections Model (ISM) (Proust et al. in Water Resour Res 45:1–16, 2009). The numerical study aims at validating the ISM under unsteady flow conditions, using classical 1D simulations as benchmark. It is experimentally found that 90 successive runs are required to get convergence of the ensemble averages of sub-section discharges and flow depth, while interfacial velocity is not fully converged after 100 runs. The influence of the inflow partition on the downstream parameters is felt along the whole flume. The ISM simulations are closer to the measurements than the classical 1D simulations. The ISM can accurately predict the time-varying flow depths and interfacial lateral discharge, and can approximate the interfacial Reynolds stresses.