The pristine lakes of Northern Patagonia, Chile, are facing an uncertain future. These are some of the largest temperate lakes in the world which have not had significant anthropogenic modifications to their watersheds. Yet with anticipated urban development and the ever-present effects of climate change, lake residents are concerned about a potential decline in lake water quality. Since 2019 the UC Davis Tahoe Environmental Research Center (TERC) has been collaborating with a Chilean Lake Advocacy NGO, Chile Lagos Limpios, to deploy the first in-situ, high-frequency hydrodynamic and water quality instrumentation in these lakes. The team is utilizing monitoring and modeling methods, previously developed by TERC to investigate the decline in the Tahoe’s renowned water clarity, in order to examine how in-lake physical and biogeochemical processes will change under forecast development and climate scenarios. The monitoring design and preliminary modelling results will be presented for three lakes in the study region.