High Mountain Lakes in the Central Andean Altiplano experienced significant fluctuations in water levels during the Late Quaternary, which have affected the composition of aquatic communities. In this study, Casiri Hembra and Casiri Macho Lakes (Northern Chile, > 4,800 m a.s.l.) sediment cores were obtained and analyzed by combination of different proxies: analyses of geochemistry, magnetic properties, and pollen assemblage, joint to ecological proxies, such as the structure of benthic macroinvertebrates, to identify environmental changes that occurred in the Altiplano region during the late Holocene, with particular emphasis on distinguishing local influences from broader regional processes and their impacts on aquatic community structure and surrounding vegetation of these isolated high-mountain lakes. Results showed a progressive change in depositional dynamics from the Late Holocene to the present, 900 years in Casiri Hembra Lake, and over 3,000 years in Casiri Macho Lake. Older sediments show a general dominance of fine-grained sediments, with episodes suggesting the influence of high-energy clastic inputs, likely reflecting episodic flooding or increased basin runoff. Recent deposits indicate the development of low-energy lacustrine conditions, increased productivity, and reduced terrigenous input. Volcanic activity of the surrounding complex was recorded. The aquatic community of Casiri Lakes shows a significant replacement of taxa, from Ostracoda and Diptera in older sediments to Anostraca Crustacea in the most recent sediments. In addition, the presence of local microhabitats for the observed community is noted. High sedimentation rates in Casiri Lakes suggest complementary depositional sources to authigenic processes, such as sustained atmospheric deposition, which likely represents a significant contribution to the sediment budget.