The photo-disinfection of water from two different wells (W1, pH: 4.6–5.1 ± 0.02) and (W2 pH: 5.6–5.7 ± 0.02) was carried out during the rainy season at Ouagadougou–Burkina Faso, West Africa. The weather variation during the rainy season significantly affects the photo-disinfection processes (solar disinfection and photo-Fenton). The dilution of the water by rainwater highly affected the chemical composition of the wells' water used in this study; very low iron contents Compared to the ones recorded during the dry season were recorded in all water samples. Both photo-disinfection processes were used to treat 25 L of water in a compound parabolic collector (CPC). None of them have shown the total inactivation of both wild enteric bacteria strains (total coliforms/E. coli and Salmonella spp.) involved in the treatment. However, the total coliforms/E. coli strains were totally inactivated during the exposure under most of the photo-Fenton treatment. Also, the remaining strains, especially those of Salmonella spp. were achieved during the subsequent 24 h of dark storage under the action of the Fenton process. Under uniquely solar radiation, total inactivation was recorded only in the total coliforms/E. coli strains. The impact of the available irradiance on the efficiency of the photo-Fenton disinfection of natural water was highlighted during the exposure under high intermittent solar radiation. The impact of the HCO3− concentration of both wells' water on the evolution of the pH during the photo-disinfection was recorded. Drastic decrease was noticed after the initial fast increase in presence of low HCO3− concentration while a steady state was observed after the increase in presence of higher concentration. The redox activities of the nitrogen components of the water during both photo-disinfection processes have led to increased concentration of nitrite in all the cases and variations were noticed in that of nitrate and ammonia.