The Darling-Baaka River has experienced significant national attention in recent years due to recurrent mass fish kills, most notably in 2018/19 and 2023. These events occurred under contrasting flow conditions; severe drought and post-flooding. Despite this contrast, dissolved oxygen depletion was a major driver of both fish kill events. In light of these events, and the mounting pressures of climate change, a better understanding of how river discharge and flow velocity affect river dissolved oxygen levels is becoming increasingly important for water managers. Our aim was to determine the effects of varying flow velocities on dissolved oxygen concentrations and the formation and breakdown of temperature and oxygen stratification. Furthermore, we estimated discharge thresholds that would maintain dissolved oxygen concentrations that support healthy fish habitats. To investigate this relationship, we measured and analysed surface and bottom water dissolved oxygen levels at ten sites within four weir pools on the Darling-Baaka River between September and April of 2023-2024 and compared them with discharge rates and flow velocities. Our findings reveal that the complex nature of water column oxygen dynamics necessitates a nuanced management approach to mitigate the risk of future fish kills.