The High Lakes Project is a multidisciplinary astrobiological investigation studying high‐altitude lakes between 4200 m and 6000 m elevation in the Central Andes of Bolivia and Chile. Its primary objective is to understand the impact of increased environmental stress on the modification of lake habitability potential during rapid climate change as an analogy to early Mars. Their unique geophysical environment and mostly uncharted ecosystems have added new objectives to the project, including the assessment of the impact of low‐ozone/high solar irradiance in nonpolar aquatic environments, the documentation of poorly known ecosystems, and the quantification of the impact of climate change on lake environment and ecosystem. Data from 2003 to 2007 show that UV flux is 165% that of sea level with maximum averaged UVB reaching 4 W/m2. Short UV wavelengths (260–270 nm) were recorded and peaked at 14.6 mW/m2. High solar irradiance occurs in an atmosphere permanently depleted in ozone falling below ozone hole definition for 33–36 days and between 30 and 35% depletion the rest of the year. The impact of strong UVB and UV erythemally weighted daily dose on life is compounded by broad daily temperature variations with sudden and sharp fluctuations. Lake habitat chemistry is highly dynamical with notable changes in yearly ion concentrations and pH resulting from low and variable yearly precipitation. The year‐round combination of environmental variables define these lakes as end‐members. In such an environment, they host ecosystems that include a significant fraction of previously undescribed species of zooplankton, cyanobacterial, and bacterial populations.