The effects of stream channel morphology, transport processes and effective discharge on the salmonid spawning habitats of Thymallus thymallus and Salmo trutta ff. were investigated within the catchment of the Gr. Mühl River, Austria. Based on field survey, one-dimensional and two-dimensional hydraulic and sediment transport modelling, the abiotic characteristics of the spawning sites have been investigated. Application of the Meyer-Peter, Müller and Shields equations for determining critical discharge and critical shear stress revealed differences in the threshold of sediment motion due to the specific grain size sorting of the surface layer, which was dominated by cobbles and sand. Suitable grain sizes for spawning were found mainly in the subsurface layer of the free-flowing sections. The findings highlighted the necessity for upstream delivery to downstream of suitable spawning material during floods. Moreover, the study demonstrates that discharge-related sediment transport does not mean a simultaneous renewal of spawning material (fine gravel, gravel) transported from upstream reaches. Thus, an effective discharge for spawning habitats was determined using a standardized deposition index (Di), based on two-dimensional sediment transport modelling. The results show that the effective discharge for spawning habitats is a useful tool for spawning habitat restoration, representing the frequency of turnover and renewal of spawning habitats over the long term. Copyright© 2010 John Wiley & Sons, Ltd.