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Water flow causes complex patterns of sediment disturbance in sand-bed streams, but effects on stream metabolism resulting from different depths of sediment scour and fill are poorly known. We assessed such effects by manually disturbing sandy sediments of 16 experimental outdoor flumes to two different depths (1 and 4 cm) during an early and a more advanced stage of stream community succession. To separate effects on heterotrophic and autotrophic metabolism, half of the flumes were permanently covered. At the early successional stage, sediment disturbance did not affect net community production (NCP), while sediment mixing reduced production independent of disturbance depth in the later stage. Microbial respiration, in contrast, was significantly stimulated when sediment was mixed to greater depth. These results suggest that disturbing sediments during early successional stages has no effect on whole-stream metabolism, whereas at later stages, deep sediment disturbance can lead to a transitory shift toward heterotrophy. The recovery time of NCP from perturbation was independent of disturbance depth. Similar trajectories observed after deep and shallow sediment disturbance indicate that delayed recovery was not simply due to mixing algae into deeper sediment layers but primarily a result of disrupting the fine structure of the surface sediment.