The global cycling of nitrogen (N) has been increasingly altered by human activity during the past century due in large part to intensified fertilizer inputs to agricultural soil. One consequence of these inputs is increased production of the N oxide trace gases, nitric oxide (NO) and nitrous oxide (N2O). Once emitted to the atmosphere, these trace gases have impacts on ozone chemistry, global warming, and N deposition. The goal of this research was to address major gaps in our understanding of the processes responsible for NO and N2O generation and in our ability to assess the impact of agricultural practices on the atmosphere. Soil pH and factors which lead to accumulations of nitrite (NO2-) were demonstrated to be of critical importance. Abiotic reactions involving nitrous acid (HNO2) were found to be primarily responsible for the NO produced during nitrification, and were partly responsible for the N2O produced. Gross production rates were well-described as functions of HNO2 concentrations and were positively correlated with soil organic matter, but were not related in a simple way to the overall nitrification rate. Temperature effects on reaction kinetics were well-described by Arrhenius relationships. Microbial reduction of NO was found to be a significant source of N2O and was described kinetically as a function of NO concentration and per cent saturation. The importance of these processes at the field-scale was demonstrated, indicating that the control of soil acidity may be an effective means of minimizing N losses. The kinetic results were incorporated into a mechanistic mathematical model which describes both steps of the nitrification sequence, pH dynamics, and diffusion of solutes and gases. Temporal patterns predicted by the model were very consistent with field and laboratory data reported here and in prior studies. Predicted emissions were highly sensitive to several parameters, including the growth rate of Nitrobacter populations, soil acid buffering capacity, and depth of fertilizer incorporation. Overall, these results demonstrate how microbial, chemical and physical factors will interact to control N oxide gas emissions. The model provides a quantitative tool for assessing the impact of agricultural practices and soil factors on NO and N2O emissions.