In this work, we studied the effect of inorganic ions occurring in natural waters on E. coli inactivation by solar and photo-Fenton processes, two crucial methods for drinking water treatment in sunny or developing countries. ${\text{H}\text{C}\text{O}}_3^{-},{\text{C}\text{l}}^{-},{\text{S}\text{O}}_4^{2-},{\text{N}\text{O}}_3^{-},{\text{N}\text{O}}_2^{-}$ and ${\text{N}\text{H}}_4^{+}$ were assessed at relevant concentrations for their inhibiting or facilitating role. The inactivation enhancement during solar disinfection (SODIS) was mainly attributed to the generation of ${\text{H}\text{O}}^{•}$ radicals produced during by excitation of ${\text{N}\text{O}}_3^{-},{\text{N}\text{O}}_2^{-}$, while the ${\text{H}\text{O}}^{•}$ of photo-Fenton may be transformed into other radical species in presence of ions. Natural organic matter (NOM) was found to enhance both processes but also to hinder most of the enhancing ions, except for ${\text{N}\text{O}}_2^{-}$; modeling with the APEX software unveiled the inter-relations in the presence of NOM, and the possible inactivation activity by ${\text{N}\text{O}}_2^{•}$. The photo-Fenton inactivation was more significantly enhanced by ions than SODIS (besides the case of ${\text{N}\text{O}}_3^{-},{\text{N}\text{O}}_2^{-}$), but both processes were found robust enough.