Thermal and oxygen stratification are common features of lakes and pools in lowland rivers with persistent stratification commonly resulting in water quality problems and reductions in available habitat. Stratification is rarely observed in upland river systems because the structure of the rivers creates turbulent flow that mixes the water column, however significant reductions in streamflow can produce stratified conditions. This study investigated the effects of flow and pool character on stratification in pools in the upper Murrumbidgee River. Six pools, ranging in depth from 3 to 8 m in the upper Murrumbidgee River were studied during the summers of 2011/2012 and 2012/2013. The 2011/2012 summer was characterised by low temperatures and high flow conditions and the 2012/2013 summer was characterised by high temperatures and moderate to low flow conditions. Dissolved oxygen and temperature were recorded at sub-daily intervals at a range of depths using sensors attached to chains to determine the vertical patterns in environmental variables over time. Results indicated that shallower pools in open valleys respond more quickly to variations in air temperatures than do deep pools in narrow valleys. This response is amplified during low flow periods. Dissolved oxygen stratification was observed in some pools in both summers, however conditions did not persist through a full diel cycle in the 2011/2012 summer. Persistent stratification was observed in the 2012/2013 summer with oxygen concentrations as low as 0.5 mg/L at depth. Weather conditions, flow and the geomorphic character of the pools appear to be the controlling influences.