Heterogeneity operates on a multitude of spatial and temporal scales and is a prominent influence on biodiversity and ecological complexity.  To investigate how spatial complexity of diatom communities, stressors, and landscapes affect water quality monitoring and management efforts, 63 sites located throughout the region, 18 sites in the Leading Creek watershed, and 24 sites in the neighboring Shade River watershed were sampled.  For investigating temporal variations, diatom communities and environmental variables were sampled yearly for three years from 17 sites throughout the region, which represented least impaired reference habitats and a variety of flow and nutrient regimes.  Bi-weekly and monthly samples were collected for exploring shorter temporal patterns, and data is currently being analyzed.  On a large regional scale, diatom communities were strongly associated with ionic composition.  Partial multiple regression and partial canonical analyses partitioned the variance among environmental, spatial, environmental-spatial, and unexplained variation.  In the Leading Creek watershed, diatom communities were affected by pH, conductivity, sulfate, and nitrate, which reflected the predominant sources of acid mine drainage and agricultural impairments.  Environmental parameters and diatom communities were variable from year to year in some streams, and more stable in others.  Spatial and temporal implications for monitoring efforts will be addressed.