Coastal zone off central Chile is characterized by high productivity associated with seasonal upwelling of nutrient rich water, but also by oxygen deficient waters. These oceanographic conditions favor the export of fresh organic matter towards deeper portions of the water column influencing microbial communities and biogeochemical conditions in the water column. Herein, we studied the dynamic of bacteria and archaea composition in the sediments and overlying water (16Sr RNA gene i-tag) and active functional nitrifying groups (qPCR) contribution in the water column during contrasting seasons. Also, oceanographic and biogeochemical conditions in the water and sediments were studied. Biogeochemical conditions presented the influence of oxygen deficient waters and the effects of ENSO during 2015 late fall. 60 phyla were detected to be present at the sediment and active in the bottom water, benthic microbial communities’ composition at phyla level shared a higher similarity compared with bottom water counterparts. Archaea (Thaumarchaeota, Euryarchaeota, Lokiarchaeota contributed >12% to the dissimilarity found among the different biomes, followed by Marinimicrobia and Nitrospinae. The contribution of active nitrifyiers, ammonia oxidizing microorganisms (archaea and bacteria) and Nitrospina sp presented a greater contribution associated with winter and late fall consisting with higher oxygenation and nutrients in bottom waters. Oxygenation generate significant changes in the water column, particularly in bottom water active microbial communities related with nitrogen cycling.