The physical habitat simulation plays an important role in environmental flow assessments, being integrated in different methodological frameworks. Although some of these methodologies presented analysis at different scales, especially the habitat simulation at the microhabitat scale has been applied globally; thus the tools and applications of meso-scale habitat simulation are not so extended. Two difficulties for a wide application of meso-scale approaches are the diverse protocols to classify meso-habitat units and the evaluation of their changes with flow. In this research, the Mesohabitat Evaluation Model (MEM) was used for the automatic identification of mesohabitat units in different flows based on 2-dim hydraulic models. The MEM identifies and classifies habitat units based on depth, mean velocity and bed shear stress. In two rivers of Spain and Austria the habitat units were visually identified, and the models were calibrated. Several approaches of calibration were applied and the performance of the MEM in the automatic identification of habitat units was evaluated. At the Cabriel River (Spain) the approach produced a good fit under mean flow conditions, while the results at the Ybbs River (Austria) were uneven; this was related to the heterogeneity of river morphology in the transversal direction. Nevertheless, the MEM provided with an automatic classification of habitats that can be related to fish suitability, and it is flexible to adapt to different mesohabitat classifications; this approach demonstrates ample perspectives in the assessment of habitat changes in Mediterranean and alpine rivers, under steady and unsteady flow conditions.