The 60-km-long pool created by the Mildura weir exhibits pronounced physical, chemical and biological gradients along its length. As the river deepens and widens downstream along the weir pool, the flow velocity decreases and the potential for thermal stratification (intensity and duration of stratification) increases. Most nutrient concentrations (TN, NOx, FRP) as well as the euphotic depth increased in the downstream direction whereas TP and turbidity decreased. The increase in bioavailable nutrients co-occurred with an increase in electrical conductivity suggesting the presence of relatively more saline groundwater inflows to the weir pool. Throughout the summer (12 December 2003-18 March 2004), with the exception of 8 days, the water column throughout the weir pool mixed completely on a diurnal basis in the deeper sections and was continuously mixed in the shallower upstream sections. This mixing substantially reduced the mean irradiance experienced by the phytoplankton near the weir. Maximum cyanobacteria concentrations were observed in the mid-weir pool where the range of conditions was most suitable. Diatom abundance increased along the most downstream 20 km of the pool where the water column was deeper and slower flowing yet still mixed completely on a diurnal basis. Peaks in cyanobacteria biomass are not expected in the lower weir pool until lower discharges promote persistent thermal stratification and increase the mean irradiance in the surface mixed layer.