To use physical habitat models to analyze and predict ecosystem potential, compositions must also be determined of the native fish community and a subset of species must be selected for model development. The development of a Reference Fish Community (RFC) is based on the Target Fish Community approach, described by Bain and Meixler (2000). A comprehensive list of species is generated from literature sources and available regional data collected on relatively intact river reaches. The species are ranked on the basis of abundance in long-term fish collection data from multiple rivers of similar character. Securing habitat for naturally occurring dominant species (ecology) should preserve the most profound characteristics of the ecosystem, providing survival conditions for the majority of the aquatic community and therefore a reference for restoration efforts. The simplest way to create a river habitat model is therefore to select the five to ten highest ranking species for model development. It can then be assumed that community structure reflects habitat structure; therefore, the most common species should indicate the most common habitat. Since habitat availability forms the structure of aquatic fauna, the affinity between the structure of the river habitat and the structure of the fish community can be used as a measure of habitat quality.
The results of MesoHABSIM creates the framework for integrative analysis of many aspects of the ecosystem. It also allows managers to recreate reference conditions and evaluate possible instream and watershed restoration measures or alterations (such as dam removals or changes in water withdrawals). From the perspective of resource managers, it not only allows for quantitative measures of ecological integrity, but also creates a basis for making decisions where trade-offs between resource use and river restoration need to be considered.