Large-scale land uses such as residential wastewater discharge and coal mining practices, particularly surface coal extraction and associated valley fills, are of particular ecological concern in central Appalachia. Identification and quantification of both large-scale land use and microhabitat alterations to ecosystems are a necessary first-step aid in mitigation of negative consequences to biota. In central Appalachian headwater streams absent of fish, salamanders are the dominant, most abundant vertebrate predator providing a significant intermediate trophic role. Stream salamander species are considered to be sensitive to aquatic stressors and environmental alterations with past research having shown linkages among microhabitat parameters, and large-scale land use such as urbanization and logging to salamander abundances. However, there is little information examining these linkages in the coalfields of central Appalachia. In the summer of 2013, I visited 70 sites (sampled three times each) in the southwest Virginia coalfields to collect salamanders and quantify stream and riparian microhabitat parameters. In an information-theoretic framework I compared the effects of microhabitat and large-scale land use on salamander occupancy and abundances. My findings indicate that dusky salamander (Desmognathus spp.) occupancy and abundances are more correlated to microhabitat parameters such as canopy cover than to subwatershed land uses. Brook salamander (Eurycea spp.) occupancy show negative associations to large-scale land uses such as percent recent mining and percent forested. Whereas Eurycea spp. abundances are negatively influenced by suspended sediments, stream bank erosion and stream substrate embeddedness. Management implications of these findings include erosion prevention and control as well as protection and management of riparian habitats. However, quantifying physical environmental quality such as stream and riparian habitat often can be quite difficult, particularly when there are time or fiscal limitations. In order to accurately assess stream and riparian habitat in a time- and cost- effective manner, the U.S. Army Corps of Engineers (USACE) developed a functional condition index (FCI) assessment for streams that measures 11 stream and riparian parameters along with watershed land use to calculate three different scores: a hydrology score, biogeochemical score, and habitat score (Noble et al 2010). Using the salamander data from 2013, I then analyzed the FCI scores using collected occupancy and abundance analyses. Both analyses supported the Habitat FCI score as it had strong correlations with both occupancy and abundance of three Desmognathus spp., and support the use of the USACE protocol for stream and riparian habitat assessment.