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Subsurface mixing of seawater and terrestrial-borne meteoric waters on carbonate landscapes creates karst subterranean estuaries, an area of the coastal aquifer with poorly understood carbon cycling, ecosystem functioning, and impact on submarine groundwater discharge. Caves in karst platforms facilitate water and material exchange between the marine and terrestrial environments, and their internal sedimentation patterns document long-term environmental change. Sediment records from a flooded coastal cave in Cozumel Island (Mexico) document decreasing terrestrial organic matter (OM) deposition within the karst subterranean estuary over the last ∼1,000 years, with older sediment likely exported out of the cave by intense storm events. While stable carbon isotopic values (δ 13 C org ranging from −22.5 to −27.1‰) and C:N ratios (ranging from 9.9 to 18.9) indicate that mangrove and other terrestrial detritus surrounding an inland sinkhole are the primarily sedimentary OM supply, an upcore decrease in bulk OM and enrichment of δ 13 C org values are observed. These patterns suggest that a reduction in the local mangrove habitat decreased the terrestrial particulate OM input to the cave over time. The benthic foraminiferal community in basal core sediment have higher proportions of infaunal taxa (i.e., Bolivina ) and Ammonia , and assemblages shift to increased miliolids and less infaunal taxa at the core-top sediment. The combined results suggest that a decrease in terrestrial OM through time had a concomitant impact on benthic meiofaunal habitats, potentially by impacting dissolved oxygen availability at the microhabitat scale or resource partitioning by foraminifera. The evidence presented here indicates that landscape and watershed level changes can impact ecosystem functioning within adjacent subterranean estuaries. 

Abstract Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium‐to‐high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science‐policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.