Most physical habitat models such as PHABSIM (Physical HABitat SIMulation) calculate the Usable Area (UA) of the river surface or the riverbed as an indicator for the available habitat for a species of interest. Although these models have been widely applied, the three dimensionality of habitat hydraulics is increasingly being recognized as an essential issue for understanding the ecological needs of aquatic organisms. This paper describes the modular toolbox HaMoSOFT (Habitat Modelling SOFTware) which quantifies the available habitat as the Usable Volume (UV) for each class of depth, flow velocity, substrate and cover and for all possible class combinations. The toolbox was calibrated in an artificial river under laboratory conditions. Optimal grids for field sampling were defined by comparing model results based on reduced sampling densities. The UV of a natural river stretch, the Schwechat River in Austria, was analysed at different discharges to assess the impact of flow changes on model outputs. UA and UV percentages were modelled for five cross-sectional datasets, one collected in the artificial river, one in the Zwalm River (Belgium) and three in the Schwechat River at different discharges. UA percentages appeared to be higher than those of UV for lower flow velocity classes in all natural rivers and for lower depth classes in all rivers. Analysis of the Usable Volumes for the three Schwechat River scenarios revealed the observed trends were independent of flow changes. The results indicate HaMoSOFT is an interesting tool to overcome some shortcomings of Weighted Usable Area (WUA) modelling. Since the UV method is a trade-off between the practical needs for model application in river management and the complexity of the three-dimensional hydraulic models, it may be a practical approach for realistic physical habitat quantification. Copyright © 2007 John Wiley & Sons, Ltd.