In this work a photo electrochemical reactor (PEC) with a compound parabolic collector (CPC) has been designed and tested for the electrochemically assisted photocatalytic (EAP) disinfection of rainwater under real sun conditions in South Africa. The reactor consisted of a Ti mesh coated with aligned titania nanotubes with a carbon counter electrode in a concentric tubular configuration, within a borosilicate glass tube with a CPC. Environmental strains of Escherichia coli and Pseudomonas aeruginosa were used. The viability of the microorganisms was analysed by culture-based and by EMA-qPCR methods. The reactor was tested under real sun during the winter in South Africa with a relatively low UV irradiance (max: 13 Wm-2). Under real sun irradiation, EAP yielded a 5.5-log10 reduction for E. coli and a 5.8-log10 reduction for P. aeruginosa for culture-based analysis. The EAP treatment also showed improved results by EMA-qPCR analysis with a 2.4-log10 reduction in gene copies for E. coli and 3.0-log10 for P. aeruginosa.