A study was undertaken to assess some effects of nitrogen fixation and bulk organic substrate removal in a New Zealand bleached kraft pulp and paper mill wastewater treatment system. A novel wastewater biological treatment system based on nitrogen fixation has been identified as having significant potential for application in full scale treatment of pulp and paper and other nitrogen deficient wastewaters. This study contributes information about the significance and role of nitrogen fixing bacteria in such a system and will benefit development and optimisation of a wastewater treatment system based on nitrogen fixation. The specific aims of the study were i) to identify the bulk organic substrates present in the mill's treatment system, ii) to study some effects of changing the wastewater composition on the processes occurring in a nitrogen fixing biological treatment system and iii) to obtain and characterise some of the nitrogen fixing microorganisms present in this system. Methanol, acetic acid and glucose accounted for approximately 43% of the soluble chemical oxygen demand entering the treatment system. The remaining 57% was unidentified in this study. Acetic acid was the first identified substrate removed from the treatment system, implicating this compound as the preferred substrate under these conditions. A laboratory continuous culture experiment demonstrated that increases in acetate and methanol concentrations in the wastewater did not affect specific substrate removal and nitrogen fixation rates in the system but may have changed the microbial population. Low biomass nitrogen results were obtained in this experiment and attributed to microbial intracellular storage of poly-β-hydroxybutyrate. Isolates were obtained from the mill's treatment system which were able to fix nitrogen under microaerophilic conditions. Four selected isolates were able to utilise methanol, acetic acid and glucose under nitrogen fixing conditions. All of these isolates removed acetic acid from a mixed carbon substrate medium before methanol and glucose, consistent with individual substrate removal found in the Tasman treatment system.