In this paper, the study area was the Inner Niger Delta (IND) in Mali, West Africa. The IND is threatened by climate change, increasing irrigation, and dam operations. 2D hydrodynamic modelling was used to simulate water levels, discharge, and inundation extent in the IND. Three different digital elevation models (DEM) (SRTM, MERIT, and a DEM derived from satellite images were used as a source of elevation data. Six different models were created, with different sources of elevation data and different downstream boundary conditions. Given that the performance of the models varies according to the location in the IND, the variable under consideration and the performance criteria, Bayesian Model Averaging (BMA) was used to assess the relative performance of each of the six models. The BMA weights, along with deterministic performance measures, such as the Nash Sutcliffe coefficient (NS) and the Pearson’s correlation coefficient (r), provide quantitative evidence as to which model is the best when simulating a particular hydraulic variable at a particular location. After the models were combined with BMA, both discharge and water levels could be simulated with reasonable precision (NS > 0.8). The results of this work can contribute to the more efficient management of water resources in the IND.