In this contribution, the validation of EMA-qPCR method for the quantification of viable Legionella spp. in water after solar treatments was carried out. EMA-qPCR was used to evaluate the different effects of several solar water disinfection processes over this bacterium, and furthermore their mode of action. Inactivation of Legionella jordanis in water by solar photocatalytic (TiO2 and TiO2/H2O2) and solar photochemical (solar/H2O2 and solar disinfection) processes have been investigated under natural sunlight. Culture-based and molecular (EMA-qPCR) techniques were systematically compared for the analysis of treated water samples. Solar tests were done under natural solar radiation (clear sky) and ambient temperature (20-35 degrees C) for 2h, using H2O2/Solar (10, 20 and 50 mg/L), TiO2/Solar (100, 200, 300, 400, and 500 mg/L) and TiO2/H2O2/Solar (100/10, 200/10, 500/10 mg/L). According to culture-based method, the best results of bacterial inactivation were obtained for 500/10 mg/L of TiO2/H2O2. The order of efficiency to reach complete inactivation was: TiO2/H2O2/solar (5 min) >TiO2/solar (15 min) approximate to H2O2/solar (15 min) > Solar only disinfection (90 min). Moreover, EMA-qPCR and culturable counting results showed a direct correlation for samples treated with TiO2/solar for those catalyst concentrations that generate a strong oxidative attack over the cell wall. EMA-qPCR results demonstrated to be a good method to detect damaged and dead cells when the treatment affects the integrity of the cell's membrane, as occurs under photocatalysis. Meanwhile for solar disinfection and solar/H2O2 (at non-toxic concentrations, <1.5 mM), where membrane integrity remained unaltered, EMA-qPCR results couldn't discriminate between alive and dead cells, even when the bacteria were not culturable. (C) 2016 Elsevier B.V. All rights reserved.