Dissolved oxygen (DO) concentrations and high temperatures are known to adversely effects fish populations in rivers. While thermal and oxygen stratification are rare under natural conditions in upland river systems significant reductions in flow caused by extractions, can result in low DO concentrations and high temperatures. The effects of flow and geomorphic character on DO concentrations and temperatures in pools was investigated between 2011 and 2014 in the upper Murrumbidgee River. Dissolved oxygen and temperature were recorded at hourly intervals in six pools ranging in depth from 3 to 7 m and known to provide important habitat for Murray cod. High water temperatures and low DO concentrations and were observed at all sites and were most common between January and March. Antecedent air temperatures and the geomorphic character of the pools were important determinants of water temperatures. Deep pools in confined bedrock reaches displayed cooler water temperatures at depth and are likely to provide fish with refuge from high water temperatures. Such deep pools were most likely to experience persistent low DO conditions, particularly at depths beyond 4 m. Flows of up to 300 ML/day had little effect on the probability of low DO concentrations at depth which means that flow manipulation is unlikely to improve DO conditions at the deepest points of the river. There is sufficient variation in pool morphology along the river to provide fish with refuge from high temperatures and low DO conditions, however fish must be able to move to access suitable conditions.