The continental shelf region off central Chile (∼36°S), 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-) 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 -2 d -1, occurred during the upwelling season (i.e. austral spring and summer), while NH 4+ removal from the water column up to -5.7 mmol m -2 d -1 during non-favorable upwelling conditions was observed (i.e., austral winter and the 1997-1998 El Niño 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 -2 d -1, 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- (-3.4±1.4 mmol m -2 d -1) and as an important denitrification site (0.6-2.9 mmol m -2 d -1) coupled with NO 3- produced by nitrification (58-97%). Other processes such as NO 3- ammonification or active NO 3- uptake by Thioploca mats could account for NO 3- uptake from the water column. © 2004 Elsevier Ltd. All rights reserved.