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High Andean vegas constitute ecologically and functionally critical wetlands, representing some of the most fragile ecosystems within the mountainous environments of the Andes. These systems sustain high levels of biological diversity and endemism, providing habitat for numerous plant and animal species that exhibit strong sensitivity to hydrological and climatic variability. In addition, they fulfill essential ecosystem functions, including regulation of water balance, provision of ecosystem services, and freshwater supply—upon which approximately 12.4 million people in central Chile depend. A comprehensive understanding of the physical conditions that govern the synchronization of the snowpack in its solid and liquid phases—closely linked to the magnitude of seasonal water storage—and its interaction with periods of carbon sequestration is fundamental for interpreting the dominant processes that regulate the functioning of these ecosystems. To this end, we conducted extensive field measurements between 2023 and 2025, integrating data from automated weather stations (AWS) with gas exchange observations obtained through an IRGASON eddy covariance system. Furthermore, we calibrated and validated two physically based models, CRHM (Pomeroy et al., 2007) and LASSLOP (Lasslop et al., 2010), using unprecedented snow–hydrometeorological and gas exchange datasets from the Subtropical Andes of Chile. This approach enabled us to characterize CO₂ fluxes, water vapor exchange, and the dynamics of surface energy balance with high resolution and reliability. The primary objective of this study is to elucidate the functioning of high Andean vegas, with particular emphasis on the energy fluxes that regulate carbon and water cycle mass balances and their linkages to biodiversity structure and dynamics. The results are intended to provide a robust scientific basis for evidencedriven management of these ecosystems and to inform the design of conservation and functional restoration strategies in the context of ongoing degradation and biodiversity loss. Our analyses demonstrate that, under favorable hydrological conditions—characterized by sustained snowmelt inputs, subsurface inflows, and prolonged soil saturation—high Andean vegas operate predominantly as carbon sinks, with an estimated annual sequestration rate of −1.28 × 10-4 Ton Eq CO2 m-2. In addition, they store subsurface water volumes of up to 250 L s-1, with extended residence times that maintain streamflow during the dry season. Conversely, perturbations to the hydrological regime—including persistent groundwater declines associated with prolonged drought, diminished snow–glacial contributions, and increasing air and soil temperatures—combined with anthropogenic pressures such as overgrazing, vehicular traffic, soil compaction, and channelization for agricultural purposes, can trigger severe and potentially irreversible losses of ecosystem functionality. These impacts manifest as sharp declines in biodiversity and a net release of CO2 to the atmosphere. This functional duality highlights the critical role of high Andean vegas in biodiversity conservation, climate change mitigation, and hydrological regulation within mountain basins. The balance between carbon sequestration and carbon emission is tightly coupled to hydrological status, vegetation condition, and the degree of ecosystem disturbance. In this context, timely, sciencebased management interventions are essential to mitigate biodiversity loss at local and regional scales, particularly given the role of these wetlands as strategic biological corridors across the Andes.