This study is based on the hypothesis that viral aggregation slows the inactivation by chemical disinfectants. This slow-down depends on the aggregate size, the concentration and the reactivity of the disinfectant. In this work we test this hypothesis by experimentally investigating the inactivation MS2 coliphage aggregates by dichloramine and PhiX174 aggregates by PAA. The experiments performed with MS2 and dichloramine show good adherence to the theory. We observed that inactivation by dichloramine was slowed by 3.4 to 13 times with aggregates of size between 420 and 580 nm, and with a dichloramine concentration varying between 3.5 and 13 mg/L. The larger the aggregates, and the higher the concentration of disinfection, the greater was the observed inhibition of inactivation due to aggregates. Comparing the inactivation of MS2 by dichloramine and by PAA, we observed that dichloramine was a stronger disinfectant, and the impact of aggregation on dichlormaine was more extensive. This permitted to verify the hypothesis that a more reactive disinfectant was more sensitive to aggregation. Our results were furthermore in good agreement with the mechanistic model for the inactivation of viral aggregates developed by Mattle et al. (2011). In contrast to MS2, results for the disinfection of aggregates of PhiX174 did not exhibit an effect of aggregation on disinfection. We hypothesize that PhiX174 viruses within aggregates were not sufficiently compact to result in inhibition of disinfection. This phenomenon was probably due to the spikes on the PhiX174 capsid. Structural features of viral aggregates thus influence their propensity to inhibit inactivation.