The Clean Water Act establishes the basic structure for regulating discharges of pollutants into the surface waters of the United States. Under the Clean Water Act, states have primary responsibility for setting, reviewing, revising, and enforcing water quality standards including the protection of biological integrity. Biological monitoring methods have been developed using aquatic macroinvertebrates, fishes and periphyton for a variety of aquatic habitats, including streams. The reliance on biological tools for stream assessments has greatly increased within the last ten years, primarily as a response to litigation based on TMDL development and impaired waters listing as outlined in the CWA. This work summarizes how species level data can be used for conservation initiatives and natural resource management. It also illustrates how biological community data informs management decisions such as road removal and other restoration efforts. This work shows how analysis of biological community data is greatly influenced by state policies and guidance for collecting, calculating and evaluating biological data which changes over time. Federal policies such as the Clean Water Act directly influence the types of biological monitoring conducted, mainly through state agencies. Litigation related to federal legislation also affects the types of stream assessment work conducted at the state level. These factors influence biological monitoring and stream assessments within the Southeast. This dissertation summarizes four years of data collection supporting management of aquatic resources on Eglin Air Force Base in the Florida Panhandle. Over 200 biomonitoring samples were collected at 127 sites across Eglin, providing baseline characteristics of the biological communities in wadeable streams. This biological data helped identify impaired sites and potential restorative actions for natural resource managers, as well as evaluate statewide changes in bioassessment criteria. Several new species records were recorded for Santa Rosa, Okaloosa and Walton counties for rare and sensitive aquatic insect taxa, including one dragonfly (Odonata) species never before described. As a result of this work, a long-term monitoring partnership program was developed, evaluated and implemented for natural resource management between the Department of Defense and the U.S. Fish and Wildlife Service.