As changes in landuse and the demand for water accelerate, regulators and resource managers are increasingly asked to evaluate water allocation against the need for protection of in-stream habitat. In the United States, only a small number of river basins have the long-term hydrograph data needed to make these assessments. This paper presents an example of how to bridge the conceptual and physical divide between GIS-based watershed modelling of basin-discharge and in-stream hydraulic habitat models. Specifically, we used a Soil and Water Assessment Tool (SWAT) model for the Hillsborough River to produce data for use in a Physical HABitat SIMulation (PHABSIM) model of the same river. This coupling of models allowed us to develop long-term discharge data in ungauged river systems based on watershed characteristics and precipitation records. However this approach is not without important limitations. Results confirm that accuracy of the SWAT-predicted hydrograph declines significantly when either the DEM resolution becomes too coarse or if DEM data are resampled to a coarser or finer resolution. This is due to both changes in the size and shape of the river basin with the varying DEMs and subsequent shifts in the proportions of land use, soils and elevation. Results show the use of 30 m DEMs produced hydrographic patterns amenable for using in-stream habitat protocols like PHABSIM model, especially where little or no hydrographic and land use information exists. Copyright © 2010 John Wiley & Sons, Ltd.