Temperature has a fundamental influence on physical, chemical and biological processing in aquatic ecosystems. River temperatures respond to a diverse array of drivers including air temperature, streamflow, and thermal inputs, but the physical template has been shown to play a significant role in structuring spatial and temporal variation in water temperature. How these factors interact to affect water temperature in complex floodplain river habitats such as those present in the Upper Mississippi River System (UMRS) is not well-studied. We used a combination of airborne thermal imagery and continuous temperature loggers deployed across aquatic area types to evaluate spatial and temporal patterns in water temperature in Navigation Pool 8 during the summer and fall of 2017. The mid-wave infrared thermal camera available for this study is not commonly used for thermal imagery acquisition over water, so we discuss accommodations that were made to account for potential interferences and describe considerations for future users interested in using the technology. We quantified thermal metrics from imagery and continuous loggers (e.g., mean, coefficient of variation, range) and compared those to hydrogeomorphic variability across aquatic areas using a Geographic Information System (GIS) dataset. Our findings showed that both temporal and spatial temperature patterns were linked to variation in depth and connectivity of aquatic areas across the pool. Despite some of the technical challenges associated with acquiring this imagery, the method shows promise for characterizing spatial variation in surface temperatures in the UMRS associated with complex physical features such as habitat rehabilitation and enhancement projects.