The pulp and paper industry has invested heavily over recent years in cleaner processing, to reduce losses and minimise its impact on the environment. Over the past fifteen years, a New Zealand integrated bleached kraft mill has undergone a comprehensive programme of upgrades to increase production, reduce water consumption and streamline its biological treatment process. Whilst the overall discharge of contaminants from the site decreased, the treatment system performance did not show a concurrent improvement as may have been expected. Reduced BOD removal, low dissolved oxygen levels, and poor solids settlability were symptomatic of phosphorus limitation in the aerated lagoon treatment system. The wastewater entering the system was found to be phosphorus limited at a BOD:P ratio of 100:0.2. Mono-ammonium-phosphate was supplemented, at approximately 30 kg P/d, to raise the phosphorus levels to a BOD:P ratio of 100:0.3. Treatment efficiencies improved very quickly after phosphorus dosage, with a 50% reduction in BOD and TSS discharge, a significant increase in dissolved oxygen levels, and improved BOD removal (85% to 93%). This case study demonstrates that whilst more closed operation can result in reduced discharge of organic loads, there may be negative impacts on the availability of nutrients for balanced biological growth.