One way to study ecological implications induced by hydropeaking represents the coupling of hydrodynamic models with habitat suitability models, in which hydrodynamic parameters are typically used to describe the physical habitat of indicator species. This article discusses the differences in habitat suitability assessment between 2D and 3D CFD modelling as input for the habitat simulation tool CASiMiR. In the first part of the article, the accuracy of the hydraulic model is evaluated by comparing the model results with laboratory (model of a laboratory channel with erodible bed) and field measurements (Valsura River, Bolzano, Italy). In the second part, the habitat suitability for the Valsura River case study (affected by hydropeaking), is analyzed comparing different approaches for the reconstruction of the velocity field (depth-averaged velocities from 2D modelling, bottom velocity field reconstruction with log-law approach from 2D modelling and bottom velocity field from 3D modelling). The results show that the habitat suitability index (HSI) using 2D or 3D hydrodynamic models can be significantly different. These differences can be ascribed to a higher capability to depict the features of the flow field with highly variable and heterogeneous boundary conditions and to the possibility to simulate the near bed hydrodynamic parameters, which are relevant for certain target species. In particular, the HSI-values using 3D hydraulics lead to larger areas of highly suitable habitats compared to 2D simulations. Moreover, considering the entire flow range of hydropeaking events, the habitat simulations with bottom flow velocities from 3D modelling provide suitable habitats over the entire flow range representing the availability of stable suitable habitats, while the habitat availability of 2D modelled flow velocity is continuously decreasing with increasing flow rates. (C) 2016 Elsevier B.V. All rights reserved.