Movement of water overlying the sediments has not been taken into consideration in most of the experiments conducted to estimate the dissolved material flux from the sediment. Even in recent experiments that incorporated the stirring motion, interpretation of the data is difficult, because the mixing rate used may be different from actual mixing rate in the field. We propose a method to estimate the in situ mixing rate that should be used to set the flow rate in a flow-through core incubation system. The flow rate is calculated from the vertical mixing rate of the water that is deduced from the heat diffusivity. Release rates of NO3+NO2–N obtained from our flow-through incubation system were higher by 1–3 orders of magnitude than those from the conventional diffusion calculation method that estimates the flux from the gradient of nutrient concentration across the sediment-water interface. Increase in NO3+NO2–N flux is considered to be due to intensification of the nitrification process as a result of an increase in dissolved oxygen (DO) supply with the motion of water. DO supply is also considered to be an important factor controlling macrofaunal abundance and consequently their excretory contributions to the fluxes of dissolved organic nitrogen as well as NH4–N. From this point of view, we strongly recommend the application of heat and mass balance theory to estimate nitrogen flux using a flow-through experimental system.