The MesoHABSIM simulation model was developed in 2000 as an enhancement of the habitat descriptions used in the physical habitat simulation model (PHABSIM). MesoHABSIM integrates system-scale assessment of ecological integrity in flowing waters with quantitative information on physical habitat distribution to simulate habitat changes at the watershed scale. The goal was better integration of physical habitat models into river management by ‘upscaling’ to address issues relevant at management levels. This paper describes the most updated version of the MesoHABSIM approach resulting from the experience gained during the application of the model in projects since 2000. Copyright © 2007 John Wiley & Sons, Ltd.