The postglacial Patagonian fjord system along the west coast of southern South America is one of the largest stretches of the southern hemisphere (SH) fjord belt, influenced by the SH westerly wind belt and continental freshwater input. This study reports a 3-year monthly time series (2017–2020) of physical and biogeochemical parameters obtained from the Reloncaví Marine Observatory (OMARE, Spanish acronym) at the northernmost embayment and fjord system of Patagonia. The main objective of this work was to understand the land–atmosphere–ocean interactions and to identify the mechanisms that modulate the density of phytoplankton. A key finding of this study was the seasonally varying asynchronous input of oceanic and estuarine water. Surface lower salinity and warmer estuarine water arrived in late winter to summer, contributing to water column stability, followed by subsurface higher salinity and less warmer oceanic water during fall–winter. In late winter 2019, an interannual change above the picnocline due to the record-high polarity of the Indian Ocean Dipole inhibited water column stability. The biogeochemical parameters (NO3−, NO2−, PO43−, Si(OH)4, pH, and dissolved oxygen) responded to the surface annual salinity variations, and oceanic water mass contributed greatly to the subsurface inorganic nutrient input. The water column N/P ratio indicated that no eutrophication occurred, even under intense aquaculture activity, likely because of the high ventilation dynamics of the Reloncaví Sound. Finally, a shift in phytoplankton composition, characterized by surface chlorophyll-a maxima in late winter and deepening of spring–summer blooms related to the physicochemical conditions of the water column, was observed. Our results support the ecosystem services provided by local oceanography processes in the north Patagonian fjords. Here, the anthropogenic impact caused by economic activities could be, in part, chemically reduced by the annual ventilation cycle mediated by the exchange of oceanic water masses into Patagonian fjords.