This study examined the drivers of water quality in a large water storage reservoir (Lake Hume) during a period of extreme drawdown (to less than 3% of capacity). During the period of extreme drawdown, the reservoir can be thought of as consisting of three separate but inter-related parcels of water. The warm surface mixed layer was about 6 m deep. Cold water inflows from the Mitta Mitta River undershot the surface mixed layer in the Mitta Mitta arm of the reservoir and flowed along the bottom of the reservoir to the Dam Wall without substantial interaction with the surface mixed layer. When inflows from the Murray River occurred, the temperature of these inflows was similar to that of the surface mixed layer within the dam and the flows appeared to move within the surface mixed layer towards the Dam Wall. These Murray River inflows were insufficient to promote total mixing of the surface and bottom waters. The Murray River arm of the reservoir became a ‘hot spot’ for nutrient production. Stratification and subsequent anoxic conditions promoted the release of nutrients – ammonium, organic N and total P – from the sediments into the overlying hypolimnion. Because the depth of the lake was relatively shallow due to the extreme drawdown, wind driven events lead to a substantial deepening (turnover) of the thermocline allowing periodic pulses of nutrients into the warm surface layer. These nutrient pulses appeared to stimulate cyanobacterial growth. Warm inflows from the Murray River then served to push the blooms formed in the Murray arm into the main body of the lake.