Little is known about carbon flux, or ecosystem metabolism, in river floodplains, particularly of dryland ecosystems, despite their potentially large and changing contributions to carbon storage and loss. We hypothesized that the region of intermittent saturation (ROIS), which is the subsurface interface between terrestrial and aquatic ecosystems, is a biogeochemical ‘hotspot’ for ecosystem respiration and carbon transformation. Groundwater mean depth and variability in the ROIS facilitate aquatic and terrestrial interaction and are in need of further study for the role they play in carbon fluxes. We have developed a novel method utilizing high-frequency sensors in groundwater wells to capture potentially quick and sporadic biogeochemical ‘hot moments’ of ecosystem respiration in the ROIS in the riparian floodplain of the Rio Grande in northern New Mexico. We deployed four EXO1 sondes, fitted with floats to maintain them within the top 1 meter of groundwater, across two floodplain sites for one year to capture biogeochemical activity in the ROIS. Each sonde is equipped with sensors to record data on temperature, conductivity, groundwater depth, turbidity, fluorescent dissolved organic matter, and dissolved oxygen (DO) in 15-minute intervals. We quantified the size of each respiration event using DO as a proxy for ecosystem respiration. We found evidence that the coefficient of variance of groundwater depth drives the size of respiration events, where higher variation in the two days preceding a respiration event significantly correlated with larger respiration events across wells and sites. Our work demonstrates the effectiveness of collecting continuous in-situ data from the ROIS and suggests that groundwater variation is a key driver in floodplain ecosystem respiration.