It is common to use environmental conditions combined with habitat delineations as proxies for ecological outcomes, such as inundation of particular wetland habitats as a proxy for vegetation persistence. An alternative is to include physical environmental conditions as drivers in process-based models that capture important events in a life cycle, thereby accounting for the environmental and biological conditions that enable those events to occur. Each approach has benefits and drawbacks and is likely to give a different assessment of the state of the target ecological responses. We modeled four iconic species of woody vegetation in the Murray-Darling Basin and considered two approaches to identifying areas favorable for each species: "habitat-based," the area of inundation in wetland types associated with each species, and "process-based," a model of the life cycle dependent on the amount, timing, and sequence of inundation and soil moisture. Calculating favorable area using inundation of identified wetland types in a habitat-based approach provided a fundamentally different assessment to using a small number of life-cycle processes (i.e., a process-based approach). Further, favorable areas often did not overlap in space, with many locations found to be favorable using one method but not the other. There may be useful information to be gleaned from comparing the two, such as identifying locations of possible contraction or expansion of the species in the future. However, it is clear that the two approaches are not equivalent and care is needed in selecting an appropriate method for a given application.