Aggregation of microbes with particles can reduce the effectiveness of ultraviolet (UV) disinfection. This study evaluated the comparative impact of dispersed spores, dispersed spores mixed with clay particles (non aggregated), spore-spore aggregates and spore-clay aggregates on 254 nm UV disinfection performance in simulated drinking waters. Spore clay aggregates were induced by flocculation with alum. It was concluded that spores within aggregates of the spore-clay system tested were protected from UV irradiation compared to non-aggregated spores and the difference between these systems was found to be statistically significant throughout UV range tested. Ultraviolet (UV) absorbance measurements are subject to significant error using a standard spectrophotometer when particles or aggregates that scatter light are present. True UV absorbance for highly turbid waters should be measured using integrating sphere (IS) spectrophotometry that allows the collection of reflected and transmitted radiation simultaneously. This is especially important when the effects of scattering impact UV disinfection, such as with the presence of aggregates. The impact of light scattering of particle-aggregated microbes on UV disinfection was evaluated by comparing standard spectrophotometer and IS absorbance measurements for UV fluence determination. Spore-clay aggregates in simulated drinking waters and spore aggregates with natural particles from raw waters were induced by flocculation. Coagulated systems significantly decreased the UV inactivation effectiveness compared to the non-coagulated system with the effects more pronounced for raw natural water. Absorbance measurement of suspensions and aggregates using standard spectrophotometry in the calculations of fluence resulted in overdosing whereas the use of IS spectroscopy did not. The results demonstrated that the use of proper absorbance measurement techniques, accounting for particle scattering, is essential for correct interpretation of the results. Includes 2 references, figures.