Lake Wivenhoe is the largest water storage reservoir in South-East Queensland and is the primary drinking water supply storage for over 600,000 people. The dam is dual purpose and was also designed to minimize flooding downstream in the city of Brisbane. In early January, 2011, record inflows were experienced, and during this period, a large number of catchment pollutants entered the lake and rapidly changed the water quality, both spatially and vertically. Due to the dendritic nature of the storage, as well as multiple inflow points, it was likely that pollutant loads differed greatly depending on the water depth and location within the storage. The aim of this study was to better understand this variability in catchment loading, as well as water quality changes during the flood event. Water samples were collected at five locations during the flood period at three different depths (surface, mid-depth and bottom), and the samples were analysed using UV and fluorescence spectroscopy. Primary inflows were identified to persist into the mid-storage zone; however, a strong lateral inflow signature was identified from the mid-storage zone, which persisted to the dam wall outflow. These results illustrate the heterogeneity of inflows in water storages of this type, and this paper discusses the implication this has for the modelling and management of such events.