Quantitative surveys of metazoan meiofauna were carried out in an upwelling region off Central Chile (36°S). During May 1997 and May 1998, coinciding with the onset and end of El Niño, five benthic stations (respectively 27, 34, 64, 88, and 120 m depth), from the middle of Concepción Bay to the edge of the adjacent continental shelf, were sampled. The sedimentary organic matter biopolymeric fraction (proteins, carbohydrates and lipids) and chloroplastic pigments were also assessed. Total meiofauna abundance and biomass increased significantly between sampling dates at the mid-bay and inner shelf sites, from 1474 ± 354 to 5035 ± 291 individuals 10 cm-2 and from 2618 ± 332 to 5241 ± 903 individuals 10 cm-2, respectively. The relative importance of copepods in the top 2 cm increased at all sites (except in the bay mouth). During May 1998, meiofauna, especially nematodes, penetrated deeper in the bay, as well as in the inner and middle shelf sediments. Changes observed in meiobenthos structure among sites and periods were attributed to the higher oxygenation of bottom waters during the summer of 1998 (i.e. El Niño conditions). This was most evident at sites such as the mid bay, where during non-El Niño years, oxygen-deficient conditions prevail. A decrease of organic matter quantity and quality, related to low primary productivity conditions in 1998 (El Niño), apparently caused few changes in meiofauna structure. A positive correlation between Thioploca and the meiofauna biomass was observed in May 1997, whereas in May 1998 no relationship was found. © 2001 Ifremer/CNRS/IRD/Éditions scientifiques et médicales Elsevier SAS.