The "Fish with Habitat Trouble" section of the National Fish Habitat Assessment is designed in a simple, summarized format to highlight how the impairment of fish habitat can and does directly affect fish in each region of the United States. The following considerations were taken to identify the subset of species used in the report. Initially a list of potential species for each region was developed by querying the American Fisheries Society’s Imperiled Fish database for species within each region that have a threat criteria of "1", which indicates that habitat loss is a reason the specie is imperiled. This list was verified and expanded by partner fisheries agencies and Fish Habitat Partnerships to ensure species were appropriate for highlighting how alterations in habitat processes lead to less fish.
The selected species can be characterized as having limited range, which makes them vulnerable to impairment on a local scale; having specialized habitat requirements, which makes them easily affected by human development; being highly migratory, which makes them vulnerable to habitat fragmentation; or having life histories, such as being long-lived and slow maturing, that do not allow easy recovery from human perturbations on the landscape. Many of the species are on State or Federal endangered/threatened/sensitive species lists. The species examples describe the geographic area of concern along with which process or habitat requirement was altered by human action, and also identify if other population issues are at work to prevent easy population rehabilitation.