Streams and rivers are subject to discharge fluctuations that may be natural or man-made, which influence biogeochemical processes and the release of CO2 to the atmosphere. Fluctuations in discharge are also associated with changing streamwater velocity that directly affects the movement of bedforms in sandy streambeds. However, bedform movement is rarely considered when studying effects of flow dynamics on biogeochemical processes. We used planar optodes during moving-bed flume experiments to quantify the effects of different flow regimes on aerobic respiration dynamics and the subsequent release of CO2. The flow regimes included constant flow (C), sinusoidal flow (S), and single peak flow events (F). Flow regimes substantially influence aerobic respiration in the streambed and, hence, the distribution of O2 and CO2 in the streambed. Hyporheic exchange flux (HEF), bedform celerity, and respiration rates increased non-linearly with streamwater velocity. It was found that HEF and CO2 evasion were highest under dynamic flow regimes S and F. However, respiration rates, the total O2 consumed, and the total CO2 produced were highest under flow regime C. This is due to low reaction rates once the streambed became stationary in the low discharge periods of flow regimes S and F. Thus, the distribution of celerities controls total respiration. Our results highlight that substantial aerobic respiration occurs even in slow-moving streambeds and that it is important to consider bedform movement when studying biogeochemical reactions in the hyporheic zone or predicting greenhouse gas emissions from catchments.