Linked hydrologic, hydraulic, and ecological models can facilitate planning and implementing water releases from reservoirs to achieve ecological objectives along rivers. We applied a flow‐ecology model, the Ecosystem Functions Model (HEC‐EFM), to the Bill Williams River in southwestern USA to estimate areas suitable for recruitment of riparian tree seedlings in the context of managing flow releases from a large dam for riparian restoration. Ecological variables in the model included timing of seed dispersal, tolerable rates of flow recession, and tolerable duration of inundation following germination and early seedling establishment for native Fremont cottonwood and Goodding's willow, and non‐native tamarisk. Hydrological variables included peak flow timing, rate of flow recession following the peak, and duration of inundation. A one‐dimensional hydraulic model was applied to estimate stage‐discharge relationships along ~58 river kilometres. We then used HEC‐EFM to apply relationships between seedling ecology and streamflow to link hydrological dynamics with ecological response. We developed and validated HEC‐EFM based on an examination of seedling recruitment following an experimental flow release from Alamo Dam in spring 2006. The model predicted the largest area of potential recruitment for cottonwood (280–481 ha), with smaller areas predicted for willow (174–188 ha) and tamarisk (59–60 ha). Correlations between observed and predicted patches with successful seedling recruitment for areas within 40 m of the main channel ranged from 0.66 to 0.94. Finally, we examined arrays of hydrographs to identify which are most conducive to seedling recruitment along the river, given different combinations of peak flow, recession rate, and water volume released. Similar application of this model could be useful for informing reservoir management in the context of riparian restoration along other rivers facing similar challenges.