Reconditioning of food processing water streams for reuse is an increasingly common water management practice in the food industry and UV disinfection is often employed as part of the water treatment. Several factors may impact the effect of UV radiation. Here, we aim to assess the impact of cell aggregation on UV inactivation kinetics and investigate if UV exposure induces aggregation. Three strains, isolated from food processing water reuse lines (Raoultella ornithinolytica, Pseudomonas brenneri, Rothia mucilaginosa) and both an aggregating and a non-aggregating strain of Staphylococcus aureus were exposed to UVC light at 255 nm using UV LED equipment. Total Viable Count and phase-contrast microscopy, coupled with image analysis, were used to compare the UV inactivation kinetics with the average particle size for a range of UV doses. Tailing effect, seen as a strong reduction in inactivation rate, was observed for all strains at higher UV doses (industrial strains ≥ 50 or 120 mJ/cm², S. aureus strains ≥ 40 or 60 mJ/cm²). The naturally aggregating strains were more UV tolerant, both within and between species. When aggregates of S. aureus were broken, UV tolerance decreased. For the processing water isolates, the lowest applied UV dose (25 mJ/cm²) significantly increased the average particle size. Application of higher UV doses obtained with longer exposure times did not further increase the particle size compared with untreated samples. For the S. aureus strains, however, no consistent change in average particle size was observed due to UV. Our results demonstrate that aggregating strains have a higher degree of protection and that UV radiation induces aggregation in some, but not all bacteria. A better understanding of the mechanisms governing microbial aggregation and survival during UV treatment could help to improve UV applications and predictions of microbial inactivation.