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Summary 1. Successful environmental flow prescriptions require an accurate understanding of the linkages among flow events, geomorphic processes and biotic responses. We describe models and results from experimental flow releases associated with an environmental flow program on the Bill Williams River (BWR), Arizona, in arid to semiarid western U.S.A. 2. Two general approaches for improving knowledge and predictions of ecological responses to environmental flows are: (1) coupling physical system models to ecological responses and (2) clarifying empirical relationships between flow and ecological responses through implementation and monitoring of experimental flow releases. 3. We modelled the BWR physical system using: (1) a reservoir operations model to simulate reservoir releases and reservoir water levels and estimate flow through the river system under a range of scenarios, (2) one‐ and two‐dimensional river hydraulics models to estimate stage–discharge relationships at the whole‐river and local scales, respectively, and (3) a groundwater model to estimate surface‐ and groundwater interactions in a large, alluvial valley on the BWR where surface flow is frequently absent. 4. An example of a coupled, hydrology‐ecology model is the Ecosystems Function Model, which we used to link a one‐dimensional hydraulic model with riparian tree seedling establishment requirements to produce spatially explicit predictions of seedling recruitment locations in a Geographic Information System. We also quantified the effects of small experimental floods on the differential mortality of native and exotic riparian trees, on beaver dam integrity and distribution, and on the dynamics of differentially flow‐adapted benthic macroinvertebrate groups. 5. Results of model applications and experimental flow releases are contributing to adaptive flow management on the BWR and to the development of regional environmental flow standards. General themes that emerged from our work include the importance of response thresholds, which are commonly driven by geomorphic thresholds or mediated by geomorphic processes, and the importance of spatial and temporal variation in the effects of flows on ecosystems, which can result from factors such as longitudinal complexity and ecohydrological feedbacks.