In this study, an oxidation model combining the mass transfer of ozone and ozonation kinetics was developed to predict the degradation of several phenolic and indolic compounds in a semi-batch reactor. The mass transfer and partition coefficients were calculated at various physical and chemical conditions. In addition, the reaction rate constants of ozone with phenolic and indolic compounds were also estimated independently using the method of competition kinetics and relative reaction-rate constants. Incorporating mass transfer and chemical reaction concepts, an oxidation model that considers side reactions between ozone and byproducts has been established using non-linear simultaneous differential equations. Thus, numerical computation is capable of simulating the degradation of phenolic and indolic compounds both in synthetic and real manure.