Agricultural runoff often contains pollutants with antagonistic impacts. The individual influence of nutrients and atrazine on periphyton has been extensively studied, but their impact when introduced together and with multiple agricultural pollutants is less clear. We simulated a field-scale runoff pulse into a riverine wetland that mimicked pollutant composition typical of field runoff of the Mississippi River Alluvial Plain. Periphyton biomass and functional responses were measured for 2 weeks along a 500 m section. Additionally, laboratory chamber assays were used to identify potential periphyton changes due to nutrients, atrazine, and their interactions. Generally, nutrients stimulated, and atrazine reduced chlorophyll a (Chl a) in chambers. In the wetland, nutrient and atrazine relationships with periphyton were weaker, and when found, were often opposite of trends in chambers. Total nitrogen (TN) was inversely related to Chl a, and total phosphorus was inversely related to respiration (R) rates. Atrazine (10-20 μg L(-1) in the wetland) had a positive relationship with ash-free dry mass (AFDM), and weakened the relationship between TN and AFDM. Wetland periphyton biomass was better correlated to total suspended solids than nutrients or atrazine. Periphyton function was resilient as periphyton gross primary production (GPP)/R ratios were not strongly impacted by runoff. However, whole-system GPP and R decreased over the 2-week period, suggesting that although periphyton metabolism recovered quickly, whole-system metabolism took longer to recover. The individual and combined impacts of nutrients and atrazine in complex pollutant mixtures can vary substantially from their influence when introduced separately, and non-linear impacts can occur with distance downstream of the pollutant introduction point.