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Despite the harsh environmental conditions in the world's oldest and driest desert, some salt flat or 'salar' environments in the Atacama Desert host standing bodies of water known as saline lakes. Evaporite minerals deposited within saline lakes result from the equilibrium of environmental, sedimentological, and biogeochemical processes that occur in the salar; consequently, these minerals are sensitive records of human activities and ecological, evolutionary, and geological changes. The objective of this study was to evaluate feedbacks between physical, chemical, and microbial processes that culminate in distinct trends in brine chemistry, saline lake morphology, and associated evaporite sediments. Using samples from the Puquios of the Salar de Llamara, Atacama Desert, northern Chile, an analysis of spatial gradients and vertical stratification of lake elemental chemistry and mineral saturation indices were integrated with a comprehensive analysis of lake morphology, including depth, slope gradient, substrate type, and mineralogy. Lake waters ranged from saline to hypersaline, and exhibited normal, well mixed and inverse stratification patterns, and results suggest a correlation with lake morphology in the Salar de Llamara. Saline to hypersaline lakes (>150 mS/cm) with stratified brines tended to have crystalline substrate and deep (>35 cm) and steep-sided lake morphologies, while unstratified lakes with lower electrical conductivity (<90 mS/cm and microbial substrates had gentle slopes and characteristically shallow depths (<30 cm). Differences in minor element chemistry (Mn and Sr) between saline lakes were observed on scales of meters to kilometers, and result in different accessory mineral assemblages. Quantification of the physical, chemical, and microbial feedbacks that produce the observed heterogeneity in these ecosystems provides key insight into the geochemical composition and lake morphology of saline lakes in extreme environments around the world., Competing Interests: Declaration of competing interest Amanda Oehlert reports financial support and travel were provided by SQM SA. R. Pamela Reid reports travel was provided by SQM SA. Erica P. Suosaari reports financial support and travel were provided by SQM SA. Alan M. Piggot reports financial support and travel were provided by SQM SA. Cecilia Demergasso reports financial support and travel were provided by SQM SA. Tianshu Kong reports travel was provided by SQM SA., (Copyright © 2022 Elsevier B.V. All rights reserved.)