The continental shelf region off central Chile ($36 1S), one of the widest and most productive areas of the eastern South Pacific, is an important site of coastal upwelling. In order to understand how seasonal and inter-annual variability in bottom-water physical and chemical conditions affect benthic nutrient regeneration and sediment characteristics in this area, ammonium (NH 4 +) and nitrate (NO 3 À) fluxes at the water–sediment interface were experimentally quantified (March 1998–April 2001), along with net NH 4 + production, potential nitrification and denitrification rates (November 1998–August 2000). NH 4 + fluxes to the overlying water up to 10.4 mmol m À2 d À1 , occurred during the upwelling season (i.e. austral spring and summer), while NH 4 + removal from the water column up to À5.7 mmol m À2 d À1 during non-favorable upwelling conditions was observed (i.e., austral winter and the 1997–1998 El Ninõ condition). The fate of the benthic N regenerated as NH 4 + appears to be controlled by the amount of labile organic carbon (here indexed as chlorophyll-a) in the surface sediment and, indirectly, by the bottom-water oxygen concentration. The balance between net NH 4 + production and potential nitrification (4.4–34.3 and 0.3–2.9 mmol m À2 d À1 , respectively) does not support the observed NH 4 + fluxes, suggesting the occurrence of other NH 4 + dissamilative (by dissolved metal or anammox) or assimilative consuming processes. Throughout the entire study period, the sediments acted as a large sink for NO 3 À (À3.471.4 mmol m À2 d À1) and as an important denitrification site (0.6–2.9 mmol m À2 d À1) coupled with NO 3 À produced by nitrification (58–97%). Other processes such as NO 3 À ammonification or active NO 3 À uptake by Thioploca mats could account for NO 3 À uptake from the water column.