The production of detrimental carbonaceous deposits in jet aircraft fuel systems results from the involvement of trace heteroatomic species in the autoxidation chain that occurs upon fuel heating. Although it has been known for many years that these sulfur-, nitrogen-, and oxygen-containing species contribute to the tendency of a fuel to form deposits, simple correlations have been unable to predict the oxidation rates or the deposit forming tendencies over a range of fuel samples. In the present work, a chemical kinetic mechanism developed previously is refined to include the roles of key fuel species classes, such as phenols, reactive sulfur species, dissolved metals, and hydroperoxides. The concentrations of these fuel species classes in the unreacted fuel samples are measured experimentally and used as an input to the mechanism. The resulting model is used to simulate autoxidation behavior observed over a range of fuel samples. The model includes simulation of the consumption of dissolved oxygen, as well as the formation and consumption of hydroperoxide species during thermal exposure. In addition, the chemical kinetic mechanism is employed with a global deposition submechanism in computational fluid dynamics (CFD) simulations of deposit formation occurring in near-isothermal as well as non-isothermal flowing environments. Experimental measurements of oxygen consumption, hydroperoxide formation, and deposition are performed for a set of seven fuels. Comparison with experimental measurements indicates that the methodology offers the ability to predict both oxidation and deposition rates in complex flow environments, such as aircraft fuel systems, using only measured chemical species class concentrations for the fuel of interest.