Abundance and production of the pelagic heterotrophic bacteria community were studied at northern Chile during winter and summer periods of 2006–2007 in relation to seasonal changes in physical and chemical variables, including the influence of a weak El Niño event. Bacterial abundance was estimated by flow cytometry and secondary bacterial production by protein synthesis after bacterial uptake of 14C-isoleucine. Bacterial biomass showed high values in the range of 2.84 at 96.6 µ g C l−1d−1 with a bacterial growth efficiency (BGE) of 37.4% in the summer of 2007, and 2.7% in the winter of 2006. High amounts of C (~1.2 to 1.8 g C m−2 d−1) were used for bacterial respiration in the upper 20 m. Environmental impact on bacterial abundance and BGE was reflected in a positive correlation with phytoplankton biomass (r2 > 0.40 P < 0.05), and a lack of correlation with temperature (P > 0.05). Seasonal differences in abundance and BGE were mainly attributed to an ‘abnormally’ warm winter of 2006, which caused a greater stratification of the water column—a weaker and much deeper oxycline. The oxycline is normally shallower (<20 m) in the zone because of the ascent of the oxygen minimum zone (OMZ) upon upwelling. Winter 2006 conditions indicated presence of a weak El Niño event. Bacteria abundance increased during this warming event, but their metabolic activity was drastically reduced, resulting in a very low BGE. Our study suggests that changes from a prevailing sub-oxic to a highly oxygenated water column could have impacted the bacterial community, thus reducing its productive capacity. Therefore, variation in vertical distribution of the OMZ forced by upwelling variability and the El Niño impact might play an important role in the dynamics of the microbial component in this highly productive upwelling system.