This study examined the relative influence of nutrients (nitrogen and phosphorus) and habitat on algal biomass in five agricultural regions of the United States. Sites were selected to capture a range of nutrient conditions, with 136 sites distributed over five study areas. Samples were collected in either 2003 or 2004, and analyzed for nutrients (nitrogen and phosphorous) and algal biomass (chlorophyll a). Chlorophyll a was measured in three types of samples, fine-grained benthic material (CHL_FG), coarse-grained stable substrate as in rock or wood (CHL_CG), and water column (CHL_S). Stream and riparian habitat were characterized at each site. TP ranged from 0.004–2.69 mg/l and TN from 0.15–21.5 mg/l, with TN concentrations highest in Nebraska and Indiana streams and TP highest in Nebraska. Benthic algal biomass ranged from 0.47–615 mg/m², with higher values generally associated with coarse-grained substrate. Seston chlorophyll ranged from 0.2–73.1 μg/l, with highest concentrations in Nebraska. Regression models were developed to predict algal biomass as a function of TP and/or TN. Seven models were statistically significant, six for TP and one for TN; r² values ranged from 0.03 to 0.44. No significant regression models could be developed for the two study areas in the Midwest. Model performance increased when stream habitat variables were incorporated, with 12 significant models and an increase in the r² values (0.16–0.54). Water temperature and percent riparian canopy cover were the most important physical variables in the models. While models that predict algal chlorophyll a as a function of nutrients can be useful, model strength is commonly low due to the overriding influence of stream habitat. Results from our study are presented in context of a nutrient-algal biomass conceptual model.