Streams are subjected to multiple anthropogenic stressors and will continue to be, far into the future. Biological monitoring is an important method for analyzing the effects of impacts on stream health and biotic communities, and to plan effective management and conservation actions. We used national monitoring data and regional data to assess the impact of geographical and environmental factors on the stability of stream communities and the selection of stream monitoring sites, respectively. For the first study, we used National Water Quality Assessment biotic community data from the United States Geological Survey to determine factors that influence the stability of stream communities. We used multiple taxa groups (i.e., fish, macroinvertebrates, and diatoms) to assess within-site community stability and used generalized additive modeling with environmental, physical, temporal, and other biologically relevant data to indicate the relative importance of factors associated with the stability of each community group. We found that turnover time was associated with comparative stability across fish, macroinvertebrate, and diatom communities, and found that the weak influence of other factors was likely clouded by the large geographic scale of our study. For the second study, we investigated criteria useful in selecting reference streams for biomonitoring when we have no previous monitoring information. We used fish, macroinvertebrate, and environmental data from 29 streams across two watersheds and three ecoregions in southeast Oklahoma to indicate factors that should be considered in reference site selection. Data were analyzed using multiple multivariate methods and an Index of Biotic Integrity. We found that ecoregions and watersheds should be considered when selecting reference site and demonstrated that using a variety of taxa and analysis methods could better describe possible impacts. Together, these two studies supplement current knowledge of how environmental, physical, and geographical factors influence multiple biotic groups in stream communities.