The knowledge of discharge hydrographs is useful for flood modelling purposes, water resource management, and the design of hydraulic structures. This paper presents a novel methodology to estimate the unknown discharge hydrograph in an ungauged river section using only water level information recorded downstream. A Bayesian procedure is coupled with a 2-D hydraulic model parallelized for GPUs. Finally, the proposed procedure has been applied to estimate inflow hydrographs in real river reaches.