AbstractHeadwater 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.