In this work, the role of dissolved oxygen in the solar and the photo-Fenton-mediated E. coli inactivation process was put under scrutiny. The effect of transient species that were produced in the presence of various natural organic matter isolates (NOM), namely Suwannee River (SR) NOM, Nordic Reservoir (NR) NOM, SR Humic acid (SRHA), and SR Fulvic acid (SRFA) was studied in detail. The role of (1) O-2 in this reaction was systematically evaluated by modifying the O-2 concentration (N-2/O-2 purging) and the matrix composition (10, 50, and 100% deuterium oxide (D2O) v/v). In the presence of NOM, (1) O-2 was generated and the enhancement of E. con inactivation rate due to charge transfer from triplet state to molecular oxygen. The comparison between SR and NR NOM showed that for these compounds, triplet state of NOM ((NOM)-N-3*), and (1) O-2 were the more favorable active species in E. coli inactivation, respectively. Also, the second order rate constants (k(E. coli)(2nd)) of E. coli with (NOM)-N-3*, and (1) O-2 were calculated by using the steady state approximation. The obtained results showed that the rate values of (1) O-2 related to NR NOM was similar to 5.6 times higher than SR NOM, while the rate values of (NOM)-N-3* for SR NOM was similar to 8.7 times higher than NR NOM. We also determined the effect of these organic matter isolates in the photo-Fenton process and its constituents (solar/Fe2+, solar/H2O2, and solar/Fe2+/H2O2). In presence of NOM, the photo-Fenton process inactivation rates increased which confirmed that the combined processes has additional pathways generated with disinfecting effect during solar exposure of bacteria.