This study presents the conceptual development and applications of the functional flows model that integrates the role of hydrogeomorphic processes and ecological functions to assess stream physical habitat. Functional flows are discharge values that serve ecological functions. The model was tuned to evaluate functionality for fall-run Chinook salmon at spawning sites located in riffles that have been rehabilitated with gravel augmentation in the Mokelumne River, and riffles that have changed due to floods in the Yuba River. Ecological functions studied are bed occupation, or periods when fish interact with the river bed (i.e. spawning, incubation, and emergence), and bed preparation, or periods when there is river bed surface reworking. The assessment of functional flows where ecological functions occur is based on the evaluation of boundary shear stress dynamics. Input variables to assess functional flows are discharge (Q), response to incremental discharge changes (represented by f in h=cQ^f), water surface slope (S), and median grain size (D₅₀). Model outputs are the calculation of number of days within a water year that present functional flows, and the identification of ranges of functional flows that provide sediment transport stages favorable for each ecological function. Model results indicate that river rehabilitation below Camanche Dam on the Mokelume River is increasing the number of days with functional flows for bed occupation, but more is needed to achieve adequate number of days for bed preparation. Results also show that natural floods on the Yuba River maintain the number of days with functional flows for spawning habitat. A comparison between both rivers shows that the Yuba presents larger ranges of functional flows, and a better balance of number of days with bed occupation and bed preparation flows. The functional flows analysis provided an objective comparative tool to assess changes in ecological functionality at hydrogeomorphically dynamic sites.