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Chromophoric dissolved organic matter (CDOM) is crucial in aquatic ecosystems, influencing light penetration and biogeochemical processes. This study investigates the CDOM variability in seven oligotrophic lakes of North Andean Patagonia using Landsat 8 imagery. An empirical band ratio model was calibrated and validated for the estimation of CDOM concentrations in surface lake water as the absorption coefficient at 440 nm (acdom440, m−1). Of the five atmospheric corrections evaluated, the QUAC (Quick Atmospheric Correction) method demonstrated the highest accuracy for the remote estimation of CDOM. The application of separate models for deep and shallow lakes yielded superior results compared to a combined model, with R2 values of 0.76 and 0.82 and mean absolute percentage errors (MAPEs) of 14% and 22% for deep and shallow lakes, respectively. The spatio-temporal variability of CDOM was characterized over a five-year period using satellite-derived acdom440 values. CDOM concentrations varied widely, with very low values in deep lakes and moderate values in shallow lakes. Additionally, significant seasonal fluctuations were evident. Lower CDOM concentrations were observed during the summer to early autumn period, while higher concentrations were observed in the winter to spring period. A gradient boosting regression tree analysis revealed that inter-lake differences were primarily influenced by the lake perimeter to lake area ratio, mean lake depth, and watershed area to lake volume ratio. However, seasonal CDOM variation was largely influenced by Lake Nahuel Huapi water storage (a proxy for water level variability at a regional scale), followed by precipitation, air temperature, and wind. This research presents a robust method for estimating low to moderate CDOM concentrations, improving environmental monitoring of North Andean Patagonian Lake ecosystems. The results deepen the understanding of CDOM dynamics in low-impact lakes and its main environmental drivers, enhance the ability to estimate lacustrine carbon stocks on a regional scale, and help to predict the effects of climate change on this important variable.