The coastal region of central Chile (36° S) is one of the most productive coastal systems, characterized by a marked seasonality in the upwelling regime, that brings subsurface waters rich in nutrient and poor in oxygen (ESSW) into the euphotic zone. This oceanographic condition depends basically on the equatorward wind strength and is modified on different time scales, with the El Niño-Southern Oscillation (ENSO) phenomenon as the main source of interannual variability in the Pacific Ocean. Here we present an effort to integrate physical and biogeochemical variability associated with in situ information and experiments at coastal stations off central Chile (36° S) in order to improve the knowledge on the pelagic-benthic coupling in this upwelling system during the warm ENSO phase or El Niño. Carbon fluxes exported from the water column to the sediments and the ammonium exchange across the sediment-water interface are discussed together with oceanographic and benthic conditions. All measurements and estimations were carried out from May 1997 until April 2001 at two stations, one located inside Concepción Bay (~28 m depth), and the other on the continental shelf at ~36° S (~88 m depth). The results show that the pelagic and benthic systems are strongly coupled off central Chile (36° S). Oceanographic variability associated with upwelling events (seasonal scale) and an El Niño event (interannual scale) was observed. The carbon fluxes exported to the sediments, the benthic conditions (i.e., quantity and quality of the sediment organic matter), and the ammonium exchange across the sediment-water interface, responded to the seasonal regime of upwelling during non El Niño years as well as to the ENSO related oceanographic variability.