Excess nitrate in water is a known environmental problem, the remediation of which can be accomplished by catalytic reduction of nitrate to N-2 and NH4+. This work presents a model for the microkinetic modeling of a system that uses a Pd-Sn/gamma-Al2O3 catalyst taking into account the inherent transport phenomena. The pH control, which was carried out by flowing CO2, was also modeled, leading to a considerably large (and stiff) system of ordinary differential equations, which was dependent on a set of empirical parameters to be fitted. This regression was conducted using a maximum statistical likelihood criterion, employing tailor-made optimization techniques. The results indicated mass-transfer effects should be considered to obtain a complete description of the reaction system, especially regarding the pH profile.