This study applies the functional flows model (FFM) that integrates hydrogeomorphic processes and ecological functions to assess physical habitat. Functional flows are discharge values that serve ecological uses. The model was adjusted to evaluate gravel-bed riffle functionality for fall-run Chinook salmon with respect to river rehabilitation on the Mokelumne River and flood-induced channel change on the Yuba River. The goal was to test if differences in ecological performance were traceable to differences in hydrogeomorphic conditions. Ecological functions studied were bed occupation (spawning, incubation and emergence) and bed preparation (river bed reworking periods)- both reliant on shear stress dynamics. Model outputs included number of days that have functional flows, ranges of functional flows that provide favourable sediment transport stages and the efficiency of a site to produce functional flows. Statistical significance of results was tested using non-parametric tests. Functional flows analyses before and after geomorphic alteration indicate that river rehabilitation on the lower Mokelume River increased the number of days with functional flows, while the Yuba River May 2005 flood increased the functional ranges of flows for the test sites. Reach-scale analyses indicated similar ecological performance at reference sites in both rivers. A comparison between both rivers showed that despite a greater geomorphic potential of the Mokelumne River sites to have functional flows, Yuba River sites actually experienced better ecological performance for fall-run Chinook salmon freshwater life stages due to greater flow availability. The FFM provided an objective tool to assess changes in ecological functionality at hydrogeomorphically dynamic sites. © 2010 John Wiley & Sons, Ltd. Copyright © 2010 John Wiley & Sons, Ltd..

The functional flows model integrates hydrogeomorphic processes and ecological functions for stream physical habitat evaluations. Functional flows are discharge values that serve ecological uses. Assessments of functional flows are based on evaluation of shear stress dynamics. The analysis is based on the occurrence of sediment transport regimes defined by threshold values of Shields stress estimated from discharge (Q), a parameter (f) governing depth response to incremental discharge changes, water surface slope (S) and media grain size (D50). As an example, the model was tuned for fall-run Chinook salmon spawning. Ecological functions studied were bed occupation (spawning, incubation and emergence) and bed preparation (river bed reworking periods)-both reliant on shear stress dynamics. A numerical experiment and sensitivity analysis using a wide range of realistic values of input variables indicated the effect of each variable on flow functionality. Combinations of S-=-0.001, 0.005 and 0.01, D50-=-0.02, 0.05, 0.1-m, f-=-0.2, 0.3, 0.4, 0.5 and four sediment transport stages produced 144 scenarios. Ranges of functional flows were greater for scenarios for low f (0.2) with low slope (0.001,0.05), for high f (0.5) with small grain size (0.02-m) and for intermediate low f (0.3) with coarse grain size (0.1-m). The functional flows model incorporates in-stream habitat processes by including metrics of hydrologic, hydraulic, geomorphic and ecologic dynamics. Model uncertainties related to input data, calculation algorithms, and model structure are analysed. Functional flows analysis can be useful in studying water management alternatives to improve habitat conditions for target species and lifestages. Copyright © 2009 John Wiley & Sons, Ltd. Copyright © 2009 John Wiley & Sons, Ltd.