Microfiltration/ultrafiltration (MF/UF) membranes and ultraviolet (UV) light disinfection serve as attractive alternative technologies to aid utilities in complying with both the LT2ESWTR and Stage 2 D/DBP. However, both technologies are limited in their ability to remove viruses and at the same time there is a lack of methods to accurately demonstrate virus removal in full-scale settings. In evaluating the efficacy of MF/UF membranes and UV disinfection systems for virus removal, appropriate surrogates are therefore required. In most cases, various surrogates are used to evaluate the removal performances of individual treatment technologies. This henceforth limits its application when multiple treatment systems are evaluated in series. In view of this, fluorescent-conjugated MS2 and F8781 microspheres were evaluated as possible surrogates for virus removal by integrated coagulation-MF/UF filtration-UV disinfection. At 5 mg Al3+/L, the highest removal of MS2-Sypro was observed, followed by MS2-AMCA, and F8781 during the coagulation-flocculation stage. During MF and UF filtration, dye surrogates provided an underestimate of virus removal except for F8781, which had a considerably smaller particle size than other surrogates. Nevertheless, MS2-SR could accurately represent AD5 during low pressure (LP) UV irradiation but MS2-AMCA existed as a more accurate representation of AD5 as compared to F8781 microspheres during medium pressure (MP) UV irradiation. MS2-SR and MS2-AMCA are therefore preferred surrogates for an integrated filtration-UV disinfection system for LP and MP UV, respectively.