Viruses in wastewater and natural environments are often present as aggregates. The disinfectant dose required for their inactivation, however, is typically determined with dispersed viruses. This study investigates how aggregation affects virus inactivation by chemical disinfectants. Bacteriophage MS2 was aggregated by lowering the solution pH, and aggregates were inactivated by peracetic acid (PAA). Aggregates were re-dispersed before enumeration to obtain the residual number of individual infectious viruses. In contrast to enumerating whole aggregates, this approach allowed an assessment of disinfection efficiency which remains applicable even if the aggregates disperse in post-treatment environments. Inactivation kinetics were determined as a function of aggregate size (dispersed, 0.55 and 0.90 µm) and PAA concentration (5-100 mg/L). Aggregation reduced the apparent inactivation rate constants 2-6 fold. The larger the aggregate and the higher the PAA concentration, the more pronounced the inhibitory effect of aggregation on disinfection. A reaction-diffusion based model was developed to interpret the experimental results, and to predict inactivation rates for additional aggregate sizes and disinfectants. The model showed that the inhibitory effect of aggregation arises from consumption of the disinfectant within the aggregate, but that diffusion of the disinfectant into the aggregates is not a rate-limiting factor. Aggregation therefore has a large inhibitory effect if highly reactive disinfectants are used, whereas inactivation by mild disinfectants is less affected. Our results suggest that mild disinfectants should be used for the treatment of water containing viral aggregates.