Two stations representing coastal and shelf environments (bay of Concepción and adjacent shelf, respectively) were sampled in order to assess benthic nitrogen fluxes. During the study period anomalously high oxygen bottom waters conditions were observed, coinciding with the 1997-1998 El Niño event. From both sites, intact sediment cores were collected for incubation experiments to directly estimate total ammonium fluxes. Pore-water chemistry was also assessed to estimate diffusive fluxes of nitrogen compounds (NH4+, NO3- and NO2-). The NH4+ flux from incubation experiments ranged from 0.55 to 2.18 mmol m-2 day-1 in the inner bay and from 1.84 to 2.14 mmol m-2 day-1 on the shelf. NO3- diffusive fluxes to the sediments were observed in the bay in March (-17 x 10-2 mmol m-2 day-1)and on the shelf in November (-2.7 x 10-2 mmol m-2 day-1), associated with the lowest NH4+ diffusive fluxes and coincident with a stronger gradient of Eh in the first centimeters of the sediments. Besides, total NH4+ fluxes lower than in normal periods were observed, suggesting the influence of less reducing conditions, consequence in turn of the lower fluxes of particulated organic material and higher dissolved oxygen in the bottom waters. These conditions were probably imposed by the El Niño event. On the other hand, and relative to previous reports, an increase of irrigation coefficients (DI) was estimated. Thus, the flux extension of other nitrogen compounds could have acquired relevance in relation to NH4+ fluxes during the study period