Pollutant effects on biofilm physiology are difficult to assess due to differential susceptibility of species and difficulty separating individual species for analysis. Also, measuring whole assemblage responses such as metabolism can mask species-specific responses, as some species may decrease and others increase metabolic activity. Physiological responses can add information to compositional data, and may be a more sensitive indicator of effect. It is difficult, however, to separate individual species for biochemical analyses. Agricultural runoff often contains multiple pollutants that may alter algal assemblages in receiving waters. It is unclear how mixtures containing potential algal growth stimulators and inhibitors (e.g., nutrients and herbicides) alter algal assemblage structure and function. In research presented here, algal biofilms were exposed to nutrients, atrazine, and their mixtures, and assemblage-level structural and functional changes were measured. Synchrotron infrared microspectroscopy (IMS) was used to isolate the biochemical changes within individual cells from a dominant species of a green alga (Mougeotia sp.), a diatom (Navicula sp.), and a cyanobacterium (Hapalosiphon sp.). At the assemblage level, mixtures generally increased algal biovolume, decreased chlorophyll a, and had no effect on metabolism or ammonium uptake. Navicula had a strong negative response to atrazine initially, but later was more affected by nutrients. Hapalosiphon responded positively to both atrazine and nutrients, and Mougeotia did not exhibit any biochemical trends. Generally, biochemical changes in each species were similar to cells experiencing low stress conditions, with increased relative protein and decreased relative lipid. IMS provided direct evidence that individual species in a natural biofilm can have unique responses to atrazine, nutrients, and mixtures. Results suggest that the initial benthic community composition should have a strong influence on the overall impact of agricultural pollutants.