Many streams within the United States are impaired due to nutrient enrichment, particularly in agricultural settings. The present study examines the response of benthic algal communities in agricultural and minimally disturbed sites from across the western United States to a suite of environmental factors, including nutrients, collected at multiple scales. The first objective was to identify the relative importance of nutrients, habitat and watershed features, and macroinvertebrate trophic structure to explain algal metrics derived from deposition and erosion habitats. The second objective was to determine if thresholds in total nitrogen (TN) and total phosphorus (TP) related to algal metrics could be identified and how these thresholds varied across metrics and habitats. Nutrient concentrations within the agricultural areas were elevated and greater than published threshold values. All algal metrics examined responded to nutrients as hypothesized. Although nutrients typically were the most important variables in explaining the variation in each of the algal metrics, environmental factors operating at multiple scales also were important. Calculated thresholds for TN or TP based on the algal metrics generated from samples collected from erosion and deposition habitats were not significantly different. Little variability in threshold values for each metric for TN and TP was observed. The consistency of the threshold values measured across multiple metrics and habitats suggest that the thresholds identified in this study are ecologically relevant. Additional work to characterize the relationship between algal metrics, physical and chemical features, and nuisance algal growth would be of benefit to the development of nutrient thresholds and criteria.