A pilot scale nitrogen (N) removal system was constructed and operated for approximately 365 days and was designed to remove inorganic total ammonia nitrogen (TAN) from solids-separated dairy manure. An anaerobic fermenter, upstream of the N removal reactor, produced volatile fatty acids (VFAs), to be used as an electron donor to fuel denitrification, and TAN at a COD:N ratio of 18:1. However, sufficient amounts of non-VFA COD was produced by the fermenter to fuel the denitrification reaction at an average NO3- removal rate of 5.3 ± 2 mg/L NO₃--N. Total ammonia N was removed from the fermenter effluent in an N removal reactor where a series of aerobic and anoxic zones facilitated aerobic TAN oxidation and anoxic NO₃- and NO₂- reduction. The minimum dissolved oxygen (DO) concentration allowing for complete TAN removal was found to be 0.8 mg/L. However, TAN removal rates were less than predicted using default nitrifying kinetic parameters in BioWin®, a biological modeling simulator, which indicated the presence of a nitrification inhibitor in fermented dairy manure. Furthermore, an N balance during the aerobic zone indicated that simultaneous nitrification-denitrification (SND) was occurring in the aerobic zone of the N removal reactor and was most apparent at DO concentrations below 1.3 mg/L. A series of nitrite generation rate (NGR) experiments confirmed the presence of an inhibitor in fermented dairy manure. A model sensitivity analysis determined that the most sensitive ammonia oxidizing bacteria (AOB) kinetic parameters were the maximum specific growth rate, , and the substrate half saturation coefficient, . Nitrifying inhibition terms of competitive, non-competitive, mixed competitive, and un-competitive were applied to the growth rate equation in BioWin® but an accurate representation of the observed TAN removal rates in the pilot scale system could not be found by adjusting the kinetic parameters alone. Reducing the default BioWin® hydrolysis rate by approximately 50% produced a more accurate calibration for all inhibition terms tested indicating that the hydrolyization of organic N in dairy manure is less than typical municipal waste water. / Master of Science