The use of remote sensing has allowed enormous progress in our understanding of biophysical processes worldwide. Despite their importance, the use of satellite bio-optical products is still limited due to optical complexity. In this study we assess the performance of the Moderate Resolution Imaging Spectroradiometer algorithm for chlorophyll-a (MODIS-OC3) and of normalized Fluorescence Line Height (nFLH), in inner waters of northern Chilean Patagonia (41 degrees-45 degrees S). Satellite data were evaluated using a compilation of in situ chlorophyll-a data collected by the CIMAR-FIORDOS program during 2003-2012. During austral spring MODIS-OC3 showed a significant relationship with in situ measurements (R-2 = 0.2, P = 0.03, F = 5.33) in comparison with winter when the relationship was non-significant. In contrast, nFLH explained a significant fraction of observed variance of Chl-a during austral winter (R2 = 0.54, P = < 0.01, F = 10.68) and this relationship was not significant in spring. Our preliminary results offer an excellent chance to understand patterns of variability of the autotrophic biomass and physiological status in optically complex interior marine ecosystems.