Northern Patagonia is one of the largest estuarine systems worldwide. It is characterized by complex geography, including islands, peninsulas, channels, and fjords. Here, the Inner Sea of Chiloe (ISC) is the largest estuarine system extending about 230 km in the meridional direction. Phytoplankton's long-term dynamics and the main physical drivers of their variability are not well understood yet. Time-space fluctuations of Chlorophyll-a (Chl-a) and Chlorophyll fluorescence (nFLH) within the ISC and their association with meteorological and oceanographic processes were analyzed using high resolution (1000 m) satellite data (2003-2019). Our results revealed a meridional Chl-a and nFLH gradient along the ISC, with higher concentrations north of the Desertores islands where the topography promotes a semi-closed system with estuarine characteristics yearlong. Satellite Chl-a and nFLH were characterized by asynchronous seasonal cycles (nFLH peaks in fall) that differed from the southern ISC where the maximum Chl-a and nFLH occurs in spring-summer. The adjacent coastal ocean influences the southern ISC, and thus, the Chl-a and nFLH variability correlated well with the seasonal variation of meridional winds. The northern ISC was clearly influenced by river discharges, which can bias the Chl-a retrievals, decoupling the annual cycles of Chl-a and nFLH. In situ data from a buoy in Seno Reloncavi reaffirmed this bias in satellite Chl-a and a higher correlation with nFLH, by which the construction of a local Chl-a algorithm for northern Patagonia is essential.