In the majority of large river systems, flow is regulated and/or otherwise affected by operational and management activities, such as ship locking. The effect of lock operation on sediment-water oxygen fluxes was studied within a 12.9 km long impoundment at the Saar River (Germany) using eddy-correlation flux measurements. The continuous observations cover a time period of nearly 5 days and 39 individual locking events. Ship locking is associated with the generation of surges propagating back and forth through the impoundment which causes strong variations of near-bed current velocity and turbulence. These wave-induced flow variations cause variations in sediment-water oxygen fluxes. While the mean flux during time periods without lock operation was 0.5 ± 0.1 g m-2 d-1, it increased by about a factor of 2 to 1.0 ± 0.5 g m-2 d-1within time periods with ship locking. Following the daily schedule of lock operations, fluxes are predominantly enhanced during daytime and follow a pronounced diurnal rhythm. The driving force for the increased flux is the enhancement of diffusive transport across the sediment-water interface by bottom-boundary layer turbulence and perhaps resuspension. Additional means by which the oxygen budget of the impoundment is affected by lock-induced flow variations are discussed.