Conservation efforts under regulatory programs such as the U.S. Endangered Species Act and Magnuson-Stevens Fisheries Conservation and Management Act seek to restore species in decline to a level where the populations are no longer in jeopardy. Key to designing effective conservation plans for the more than 2,500 species currently managed by these two U.S. programs is the establishment of realistic restoration targets given changes in habitats and ecosystems. Accomplishing this is difficult, particularly for populations that have experienced significant habitat alterations. We developed and assessed an approach for establishing quantifiable goals for the recovery of a threatened species by (1) estimating historical population biomass prior to directed fishing, (2) identifying large-scale habitat modifications that limit available critical habitat, (3) assessing the relationship between historical baselines, habitat characteristics, and extant available habitat, and (4) using these relationships to inform recovery efforts in rivers where traditional stock assessment methods are not possible. In our case study of Gulf Sturgeon Acipenser oxyrinchus desotoi, we found that the current population levels in four of the seven river systems in the recovery plan are likely at or exceeding the mean carrying capacity, given the current levels of available habitat. In the remaining three rivers, extant Gulf Sturgeon populations are likely below their estimated carrying capacity levels. Our approach is of management importance because it establishes realistic recovery criteria through the assessment of changes in habitat from historic to present levels and is widely applicable across a species' range. An important application of this approach is to assess the potential benefits to fish species from management actions, such as dam removal or spawning habitat restoration, that are designed to restore habitat and promote species recovery.