A robust parameter set (ROPS) selection framework for an unsteady flow model was developed by combining Pareto optimums obtained by outcomes of model calibration using multi-site observations with the minimax regret approach (MRA). The multi-site calibration problem which is a multi-objective problem was solved by using an aggregation approach which aggregates the weighted criteria related to different sites into one measure, and then performs a large number of individual optimization runs with different weight combinations to obtain Pareto solutions. Roughness parameter structure which can describe the variation of Manning’s n with discharges and sub-reaches was proposed and the related coefficients were optimized as model parameters. By applying the MRA which is a decision criterion, the Pareto solutions were ranked based on the obtained regrets related to each Pareto solution, and the top-rated one due to the lowest aggregated regrets of both calibration and validation was determined as the only ROPS. It was found that the determination of variable roughness and the corresponding standardized RMSEs at the two gauging stations varies considerably depending on the combinations of weights on the two sites. This method can provide the robust parameter set for the multi-site calibration problems in hydrologic and hydraulic models.