Using a two-dimensional simulation analysis, we investigated the effects of sediment flushing on denitrification and the implications for two methods commonly used to measure denitrification in intact sediment cores: the N2:Ar-ratio method and isotope pairing technique (IPT). Our simulations of experimental chamber incubations showed that advective flushing of the sediment can significantly increase sediment denitrification driven by NO3– from the water column (up to a factor of 5), but that nitrification and coupled nitrification-denitrification is reduced under conditions of sediment flushing (up to a factor of 6). N2 fluxes across SWI may differ significantly from actual rates of denitrification for periods lasting from 1 up to more than 5 d after changes in parameters such as sediment flushing rate and water column NO3– concentrations. Simulations of the isotope pairing technique, showed that the rate of labeled N2 production, after the addition of 15NO3– may take up to ~24 h to reach steady state, depending on NO3– concentrations in the water column and sediment flushing rate. Measurements of denitrification in sand using IPT confirmed that short term incubations (11 h) underestimated the actual denitrification. Furthermore, model simulations were able to give a good estimate of measured N2 fluxes across SWI at different flushing rates under non–steady state conditions, confirming the ability of the model to realistically simulate experimental situations.