Concepción Bay is a socio-economic and ecologically important embayment whose hydrographic variability has been historically regulated by wind-modulated seasonal upwelling events during spring–summer and by freshwater from precipitation and river discharges during fall–winter. This system is subject to several anthropogenic and environmental strains due to the intense port activity and the increasing occurrence of extreme natural events. This study determines a new hydrographic regime and characterizes and analyzes the biogeochemical response of the water column to changes in rainfall and upwelling patterns. Despite the intrusion of nitrate-rich upwelled waters that enhance biological productivity remains more intense during spring–summer, the system remains fertilized year-long due to the occurrence of persistent upwelling pulses during fall–winter. The hydrographic structure presented a two-layer water column that was stratified thermally in spring–summer and primarily by freshwater inputs in fall–winter. Nevertheless, the regular pattern of the rainfall has changed (a decrease in precipitation and an increased frequency of extreme rainfall events), together with recurrent upwelling-favorable wind pulses during the non-upwelling season. This new regime has altered the seasonality of the physicochemical conditions and the structure of the microplanktonic communities, with productive and sanitary implications affecting the biogeochemical status of CB.