Eddy correlation (EC) measurements in the benthic boundary layer (BBL) allow estimating benthic O2 uptake from a point distant to the sediment surface. This noninvasive approach has clear advantages as it does not disturb natural hydrodynamic conditions, integrates the flux over a large foot-print area and allows many repetitive flux measurements. A drawback is, however, that the measured flux in the bottom water is not necessarily equal to the flux across the sediment-water interface. A fundamental assumption of the EC technique is that mean current velocities and mean O2concentrations in the bottom water are in steady state, which is seldom the case in highly dynamic environments like coastal waters. Therefore, it is of great importance to estimate the error introduced by non steady state conditions. We investigated two cases of transient conditions. First, the case of transient O 2concentrations was examined using the theory of shear flow dispersion. A theoretical relationship between the change of O 2concentrations and the induced vertical O2flux is introduced and applied to field measurements showing that changes of 5-10 μm MO2h-1result in transient EC-fluxes of 6-12 mmol O 2m-2d-1, which is comparable to the O2 uptake of shelf sediments. Second, the case of transient velocities was examined with a 2D k-ε turbulence model demonstrating that the vertical flux can be biased by 30-100% for several hours during changing current velocities from 2 to 10 cm s-1. Results are compared to field measurements and possible ways to analyze and correct EC-flux estimates are discussed. © 2013. American Geophysical Union. All Rights Reserved.