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°-45ºS). 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 (R2 = 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 =