Colored dissolved organic matter (CDOM) is an indicator and optical proxy of terrestrial processes such as land use with allochthonous material fluxes, biogeochemical cycles, and water quality in coastal zones influenced by rivers. However, the role of land use changes on the spatial and temporal availability of CDOM has been poorly explored in Chile. Here, we studied two watersheds with similar climates and contrasting land use patterns in northern Patagonia considering the sampling of CDOM in their estuarine and adjacent coastal ocean. An empirical algorithm with the coefficients adjusted to our study areas to estimate CDOM was applied to Landsat 7 and 8 images to examine temporal variability of CDOMest from 2001 to 2011 and 2013–2020. Our results showed an increasing trend of CDOMest in both areas. Different trends in land use patterns between the two watersheds showed a significant correlation with CDOMest and contrasting associations with environmental variables. Higher humification was found in Yaldad in comparison with Colu. In both areas, allochthonous materials predominated, especially during austral spring according to the low values of the Fluorescence Index (FI). Our results highlight the potential of CDOMest to parameterize biogeochemical cycling models and to further understand the dynamics of CDOM in coastal ecosystems.