We analyzed the transverse pattern of vegetation along a reach of the Fremont River in Capitol Reef National Park, Utah, USA using models that support both delineation of wetland extent and projection of the changes in wetland area resulting from upstream hydrologic alteration. We linked stage-discharge relations developed by a hydraulic model to a flow-duration curve derived from the flow history in order to calculate the inundation duration of 361 plots (0.5 × 2 m). Logistic regression was used to relate plant species occurrence in plots to inundation duration. A weighted average of the wetland indicator values of species was used to characterize plots as Aquatic, Wetland, Transitional, or Upland. Finally, we assessed how alterations in the flow duration curve would change the relative widths of these four zones. The wetland indicator values of species and the wetland prevalence index scores of plots were strongly correlated with inundation duration. Our results support the concept that plants classified as wetland species typically occur on sites inundated at least two weeks every two years. The portion of the riparian zone along the high-gradient study reach of the Fremont River that satisfied the vegetation criterion for a regulatory wetland was narrow (2 m wide). Both the unvegetated Aquatic zone (7.8 m) and the Transitional zone (8 m) were substantially wider. The Transitional zone included the maxima of several species and was, therefore, not merely a combination of elements of the Wetland and Upland zones. Multiplicative increases or decreases in streamflow regime produced a wetter, or drier, bottomland vegetation, respectively. Systematic reductions in flow variability reduced the width of both the Wetland and Transitional zones and increased the width of the Upland zone. Our approach is widely applicable to inform water management decisions involving changes in flow regime.