The Mary River, in the Australian wet/dry tropics, flows seasonally to inundate a coastal floodplain. In the dry season, the river reduces to a series of disconnected lakes located along the main river channel. This paper examines the impact of riverine inflow, at the beginning of the wet season, on the limnology of Shady Camp Lake, and addresses broader water quality management issues. The first wet season flow of Mary River carried a high biological oxygen demand that reduced the lake's oxygen concentration. The resulting hypoxic conditions prompted fish avoidance behaviour and caused the death of at least 200 fish. There is no evidence of any direct anthropogenic pollution causing the event. After reaching near anoxic conditions, dissolved oxygen concentrations recovered several weeks later, although they remained low. The water quality of the Mary River was characterized by an initial pulse of water with high concentrations of organic carbon, suspended particulate material, colour, total nitrogen and total phosphorus. Phytoplankton biomass, measured as chlorophyll a, did not increase because of nitrogen limitation attributed to low nitrate and ammonia concentrations in the inflow waters. The low concentrations of available nitrogen were probably a result of denitrification, which would have been enhanced by the warm temperatures and low oxygen concentrations. The oxygen sag in Shady Camp Lake caused by the inflow of the Mary River exemplifies the vulnerability of floodplain channel lakes to riverine waters and underscores the need to manage catchment practices to minimize the concentration of labile organic material in the river and its associated oxygen demand.