In this study the photocatalytic inactivation of Escherichia coli (E. coli) and Enterococcus sp. wild strains was carried out using as photocatalyst boron-doped ZnO (B-ZnO). The photocatalytic performance of this material was compared with two commercial catalysts: ZnO and TiO2. Furthermore, the control processes of solar disinfection (SODIS) and stirring were evaluated. The performance of the catalysts was evaluated under darkness and solar simulated irradiation. Logarithmic units of inactivation and concentration of Zn2+ release during the experiments were determined. The photocatalytic inactivation of the strains was adjusted to a log-linear shoulder or tail kinetic model. To maximize the kinetic constant and determine the catalyst with the best photocatalytic performance, a desirability function was applied. Under darkness, stirring and TiO2 in suspension did no present effect in the population of both bacteria. A reduction of 1-log unit of E. coli was observed in the processes with ZnO and B-ZnO on darkness. However, Enterococcus sp. only was inactivated in darkness using B-ZnO, reaching 1.5-log. The increase of the antimicrobial effect of B-ZnO was attributed to Zn2+ release and the formation of acid sites promoted by B3+ ions in the B-ZnO catalyst. Under solar simulated irradiation, E. coli and Enterococcus sp. reached 6-log and 3-log respectively during 180 min of exposure without catalyst. The photocatalytic inactivation of E. coli was negligible using TiO2 catalyst, while heterogeneous photocatalysis using ZnO and B-ZnO materials reached 6-log during 30 min and 60 min of lighting, respectively. The photocatalytic inactivation of E. coli using ZnO exhibited higher kinetic constant value (1.12 min−1) compared to that obtained with doped B-ZnO (0.23 min−1). In the case of the photocatalytic inactivation of Enterococcus sp., 3-log in 180 min was reached using B-ZnO (0.22 min−1) while 1-log was attained using ZnO (0.02 min−1) and TiO2 (0.04 min−1). From desirability function, the maximization of the kinetic constants of inactivation of E. coli and Enterococcus sp. allowed selecting the B-ZnO as the best material due to its enhanced photocatalytic antimicrobial activity against both strains.