Patagonia is commonly seen as an exceptionally pristine area because of its wildlife and practically unpolluted waters. However, during the twentieth century the burning of natural forests was one of the most important human activities in Northern Chilean Patagonia. Some estimations indicate that three million hectares were burned during the first three decades of the century. Hence the objective of this study was to evaluate the impacts of the historical fires in Lake Burgos (45A(0)42'S) and Lake Thompson (45A(0)38'S) in Chilean Patagonia. The impact was measured by evaluating chironomid assemblage since they are sensitive enough to be used as an indicator of aquatic ecosystem health. Fires have a direct and drastic effect on a lake watershed but also indirectly affect a lake ecosystem, changing sedimentation patterns or increasing nutrient inputs. In the studied lakes the periods with higher prevalence of fires were identified by charcoal analysis, while organic matter and magnetic susceptibility allowed the confirmation of pre-fire and post-fire periods. The chironomid composition was evaluated through a PCA and an analysis of similarity (ANOSIM) to test the significance among periods while a Detrended Correspondence Analysis was applied to the chironomid assemblage downcore to assess compositional structure and taxa turnover. In Lake Burgos the ANOSIM test indicated significant differences between the pre-fire and fire periods (p < 0.05), while in Lake Thompson differences were not significant. However, in Lake Thompson the PCA clearly separated the pre-fire from the fire period but not the fire from the post-fire periods. In both lakes chironomid composition changed in relation to the period of higher prevalence of fires, which in turn implies catchment changes, pollution, and other anthropogenic impacts. Particularly a marked change in mesotrophic/eutrophic taxa was detected, reflecting an increase in nutrient input due to deforestation. Our findings point out that the lacustrine ecosystems are still affected by the impact of fires and the subsequent increase in nutrient supply that occurred almost 50 years ago. No sign of reverting to pre-disturbance conditions was observed, which makes these lakes highly sensitive to current human-induced impacts.