Data on the hydrodynamics of inflows into Darwin River Reservoir (DRR) and Manton River Reservoir (MRR) are described in respect of seasonal changes in entrained inflows. Both reservoirs are located near Darwin in the wet-dry tropics. During the transition period leading to the onset of the monsoon season (the ‘build-up’) and the monsoonal period proper, entrained inflows are clearly evident in both reservoirs but show high variation in their position in the water column. This position is largely determined by the density of inflow combined with the strength of stratification and the location of the thermocline in each reservoir’s water column. These factors play a core role in the neutral density intrusion point of inflows in the reservoirs. Seasonally variable inflow density and the large variations in the strength of stratification and its persistence at this time year have a significant influence on the transport time of potential pathogens to each reservoir’s offtake and thence to the Darwin and regional water supply. Detailed hydrodynamic modelling will be required to accurately describe these processes and provide accurate information to water supply managers.