In this comparative study, the impact of two microbial protective mechanisms against simulated UVA disinfection was assessed by using protocols previously developed for UVC disinfection assays. (i) The impact of natural microorganism aggregation and attachment to particles was assessed by targeting total coliform bacteria in natural surface water samples. (ii) The impact of bacteria internalisation by zooplankton was assessed by using C. elegans nematodes as a model host and E. coli as a bacterial target for UVA inactivation. Dispersion of natural aggregates by blending prior to UVA exposure was shown to enhance the inactivation rate of total coliforms as compared to untreated raw water. Removal of particles by an 8-microm membrane filtration did not improve UVA disinfection efficiency. Twenty-four per cent of the highest applied UVA fluence was found to reach internalised E. coli in nematodes. Both aggregation and internalisation showed similar impact as protective mechanisms against UVA and UVC bacterial inactivation.