Nutrients in pulp and paper mill effluent (PPME) have been implicated in increased periphyton chlorophyll a (chl a) downstream of discharges. These findings are largely based on short-term studies conducted in artificial stream channels or mesocosms and often in oligotrophic systems, and it is unclear if long-term chl a patterns in higher-nutrient systems would show similar response. We conducted a long-term study of 4 receiving waters (Codorus Creek, Pennsylvania; the Leaf River, Mississippi; and the McKenzie and Willamette rivers, Oregon) in which periphyton samples and associated data on water quality (nitrogen and phosphorus concentrations, pH, color, and conductivity) and 2 physical habitat variables (depth and current velocity) were collected over an 8-y period from multiple sites upstream and downstream of PPME discharges. Study streams represented different ecoregions, warm- and coldwater systems, gradients of in-stream effluent concentration (<1–33%), and mill process types. General Linear Models examining the main and interaction effects of site, season, and year on periphyton chl a for each of the 4 streams showed periphyton chl a downstream of the PPME discharge in Codorus Creek and the McKenzie River was greater at some, but not all upstream sites, suggesting these differences may be due to factors other than PPME. Mean periphyton chl a ranged from <1 to 285 mg/m² across streams, with relatively consistent site patterns across seasons and years. Overall, chl a in the spring and summer was greater than in the fall in Codorus Creek and on sand substrates in the Leaf River, with overall differences across years seen on rare occasions in the Leaf and Willamette rivers. Regression models examining environmental-chl a relationships explained 45.4% and 30.2% of variation in periphyton chl a in the McKenzie River and Codorus Creek, respectively, and <10% in the Leaf and Willamette rivers. Physical variables (stream depth and current velocity) were the most important model variables in the McKenzie River, while total nitrogen and color were of greatest importance in Codorus Creek. The findings of this study demonstrate the inherent variability of chl a standing crops, highlight the complexity of lotic periphyton communities, and reiterate the importance of long-term, multi-season studies in elucidating spatial and temporal patterns.