The variation in the matrix composition can lead to the use of inadequate oxidant dose and disturb a correct ozone treatment. The aim of this study was to model the ozone disinfection process of secondary effluents in presence of carbonate and nitrate using metal ozonation catalysts. The biological indicator used was the Escherichia coli. The ROH,O3 concept was applied to quantify and compare the E. coli inactivation by the radical pathway. The metals Fe and Zn caused a significative improvement on ROH values (p < 0.05) even in the presence of the •OH radical scavengers (carbonate and nitrate). The modelling results based on ROH values demonstrate that E. coli inactivation can be predicted satisfactory (R2 > 0.94–0.99), being a useful tool for the generalized prediction of disinfection by ozone. The presence of metals inhibited significantly bacterial regrowth (p < 0.05) even in the scavengers presence.