AbstractThe transition area between rivers and their adjacent riparian aquifers, which may comprise the hyporheic zone, hosts important biochemical reactions, which control water quality. The rates of these reactions and metabolic processes are temperature dependent. Yet the thermal dynamics of riparian aquifers, especially during flooding and dynamic groundwater flow conditions, has seldom been studied. Thus, we investigated heat transport in riparian aquifers during 3 flood events of different magnitudes at 2 sites along the same river. River and riparian aquifer temperature and water‐level data along the Lower Colorado River in Central Texas, USA, were monitored across 2‐dimensional vertical sections perpendicular to the bank. At the downstream site, preflood temperature penetration distance into the bank suggested that advective heat transport from lateral hyporheic exchange of river water into the riparian aquifer was occurring during relatively steady low‐flow river conditions. Although a small (20‐cm stage increase) dam‐controlled flood pulse had no observable influence on groundwater temperature, larger floods (40‐cm and >3‐m stage increases) caused lateral movement of distinct heat plumes away from the river during flood stage, which then retreated back towards the river after flood recession. These plumes result from advective heat transport caused by flood waters being forced into the riparian aquifer. These flood‐induced temperature responses were controlled by the size of the flood, river water temperature during the flood, and local factors at the study sites, such as topography and local ambient water table configuration. For the intermediate and large floods, the thermal disturbance in the riparian aquifer lasted days after flood waters receded. Large floods therefore have impacts on the temperature regime of riparian aquifers lasting long beyond the flood's timescale. These persistent thermal disturbances may have a significant impact on biochemical reaction rates, nutrient cycling, and ecological niches in the river corridor.