Hot summer conditions and concurrent low river flows can elevate water temperatures beyond the thermal optima of fishes, resulting in physiological stress. During these times, fish often seek refuge from thermal stress in patches of relatively cool water, such as those created where groundwater seeps through the hyporheic zone into surface water. These groundwater-fed cold-water patches can, however, be ephemeral in nature and low in dissolved oxygen, potentially limiting their value as thermal refuges. Here, we combined continuous thermal monitoring with repeated fish surveys to track the temporal dynamics of groundwater-fed cold-water patches and assess their use by cold-water adapted brown trout (Salmo trutta). The cold-water patches we identified were ephemeral and active only during low-flow conditions, which coincided with elevated temperatures in surrounding habitats. However, instead of finding refuge within the coldest available waters as expected, brown trout avoided cold but hypoxic habitats in favour of slightly warmer habitats that maintained adequate oxygenation. Thus, the value of a thermal refuge cannot be assessed by its temperature alone. Furthermore, we demonstrate that identifying and conserving thermal refuges requires longer-term monitoring to account for their potentially ephemeral nature.