Enhanced stream greenhouse gas emissions at night and during flood events

Abstract Headwater streams play a large role in aquatic greenhouse gas emissions. Carbon dioxide (CO2) and dissolved oxygen in streams often undergo changes through diel cycles. However, methane (CH4) and nitrous oxide (N2O) have unknown diel dynamics. Here, we reveal consistent patterns in CO2, CH4, and N2O over diel cycles and during flood events using high‐frequency continuous observations in a subtropical headwater stream. Diel cycles were most pronounced during baseflow. Increased nighttime discharge due to higher groundwater inputs enhanced gas transfer velocities and concentrations. Overall nocturnal emissions were 31%, 68%, and 32% greater than daytime for CO2, CH4, and N2O, respectively. Floods dampened diel signals. If both flood events and diel patterns are neglected, estimates of greenhouse gas emissions from headwaters may be greatly underestimated. Overall, CH4 and N2O emissions from headwater streams may be underestimated by ~ 20–40% due to a lack of observations during nighttime, floods, and in warmer climates.