Increased sea ice melt alters vertical surface-mixing processes in Arctic seas. More melt water strengthens the stratification, but an absent ice cover also exposes the uppermost part of the water column to wind-induced mixing processes. We conducted a field study in the Barents Sea, an Arctic shelf sea, to examine the effects of stratification and vertical mixing processes on 1) the upward nitrate flux (into surface layers <65 m) and 2) the downward flux of particulate organic carbon (POC) to ≤200 m. In the Arctic-influenced, drift ice-covered northern Barents Sea, we found a low upward nitrate flux into the surface layers (<0.1 mmol nitrate m–2 d–1) and a moderate downward POC flux (40–200 m: 150–250 mg POC m–2 d–1) during the late phase of a peak bloom. A 1-D residence time calculation indicated that the nitrate concentration in the surface layers constantly declined. In the Atlantic-influenced, ice-free, and weakly stratified southern Barents Sea a high upward nitrate flux was found (into the surface layers ≤25 m: >5 mmol nitrate m–2 d–1) during a post bloom situation which was associated with a high downward POC flux (40–120 m: 260–600 mg POC m–2 d–1). We suggest that strong wind events during our field study induced vertical mixing processes and triggered upwards nitrate flux, while a combination of down-mixed phytoplankton and fast-sinking mesozooplankton fecal pellets enhanced the downward POC flux. The results of this study underscore the need to further investigate the role of strong, episodic wind events on the upward nitrate and downward POC fluxes in weakly stratified regions of the Arctic that may be ice-free in future.