The disinfection of effluents has been considered the main step to inactivate pathogenic organisms to prevent the spread of waterborne diseases. The variation in the matrix composition can lead to the use of inadequate oxidant dose and disturb a correct treatment. The objective of this study was to develop a simple and practical mathematical model to simulate the disturbance of inorganic anions (CO32-/HCO3- and NO3-) during secondary effluent disinfection by UV/H2O2 and UV/O3. The pathogenic agents chosen for this study were total coliforms and E. coli. To build the mathematical model, a modification of the Chick model (referred to as 'Modified Chick Model') was proposed by employing a weighted average in the calculation of the kinetic constant. Both treatments were affected by the presence of the anions. However, with the highest NO3- concentration, less inhibition of disinfection was observed in the UV/H2O2. The use of the arithmetic means to calculate the value of k, as indicated by the Chick model, demonstrates a lesser precision in the prediction of the microorganisms' concentrations. On the other hand, using the Modified Chick Model, a better prediction of the inactivation of the microorganisms was obtained, which can be confirmed by the validation performed.