Decisions about reach-scale river rehabilitation for the purposes of flood protection and ecological enhancement require prediction of the possible consequences of management alternatives. To provide such predictions, an integrative model is necessary that represents the cause–effect relations between rehabilitation options and morphological, hydraulic and ecological consequences. This paper describes the morphological and hydraulic submodel of such an integrative model. This submodel is further subdivided into four modules predicting: (1) channel morphology, (2) flooding (dike overtopping, floodplain flooding and bed moving floods), (3) velocity and depth distribution and (4) riverbed siltation. Model relationships come from results reported in the literature and new data analyses. By using quantities that are all either readily available or easily predictable for changed conditions, the model should be widely applicable, even for data-limited situations. The overall model is implemented as a probability network to facilitate estimation of uncertainties in model results. An application of the model to a reach of the Thur River in Switzerland demonstrates its utility for predicting morphological and hydraulic consequences of a planned river widening. The full integrative model, including ecological endpoints, will be used together with quantitative assessments of stakeholder preferences to support rehabilitation decisions for a number of Swiss rivers. Copyright © 2007 John Wiley & Sons, Ltd.