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Abstract Nitrate legacy is affecting groundwater sources across the tropics. This study describes isotopic and ionic spatial trends across a tropical, fractured, volcanic multi‐aquifer system in central Costa Rica in relation to land use change over four decades. Springs and wells (from 800 to 2,400 m asl) were sampled for NO₃⁻and Cl⁻concentrations, δ¹⁸O_water, δ¹⁵N_NO3, and δ¹⁸O_NO3. A Bayesian isotope mixing model was used to estimate potential source contributions to the nitrate legacy in groundwater. Land use change was evaluated using satellite imagery from 1979 to 2019. The lower nitrate concentrations (<1 mg/L NO₃⁻N) were reported in headwater springs near protected forested areas, while greater concentrations (up to ∼63 mg/L) were reported in wells (mid‐ and low‐elevation sites in the unconfined unit) and low‐elevation springs. High‐elevation springs were characterized by low Cl⁻and moderate NO₃⁻/Cl⁻ratios, indicating the potential influence of soil nitrogen (SN) inputs. Wells and low‐elevation springs exhibited greater NO₃⁻/Cl⁻ratios and Cl⁻concentrations above 100 μmol/L. Bayesian calculations suggest a mixture of sewage (domestic septic tanks), SN (forested recharge areas), and chemical fertilizers (coffee plantations), as a direct result of abrupt land use change in the last 40 years. Our results confirm the incipient trend in increasing groundwater nitrogen and highlight the urgent need for a multi‐municipal plan to transition from domestic septic tanks to regional sewage treatment and sustainable agricultural practices to prevent future groundwater quality degradation effectively. 

Abstract This Scientific Briefing presents results from a nearly 10‐year hydrometric and isotope monitoring network across north‐central Costa Rica, a region known as a headwater‐dependent system. This monitoring system has recorded different El Niño and La Niña events and the direct/indirect effects of several hurricane and tropical storm passages. Our results show that El Niño‐Southern Oscillation (ENSO) exerts a significant but predictable impact on rainfall amount anomalies, groundwater level and spring discharge, as evidenced by second‐order water isotope parameters (e.g., line conditioned‐excess or line‐conditioned (LC)‐excess). Sea surface temperature anomaly (El Niño Region 3) is correlated with a reduction in mean annual and cold front rainfall across the headwaters of north‐central Costa Rica. During El Niño conditions, rainfall is substantially reduced (up to 69.2%) during the critical cold fronts period, limiting groundwater recharge and promoting an early onset of minimum baseflow conditions (up to 5 months). In contrast, La Niña is associated with increased rainfall and groundwater recharge (up to 94.7% during active cold front periods). During La Niña, the long‐term mean spring discharge (39 Ls⁻¹) is exceeded 63–80% of the time, whereas, during El Niño, the exceedance time ranges between 26% and 44%. The regional hydroclimatic variability is also imprinted on the hydrogen and oxygen isotopic compositions of meteoric waters. Drier conditions favoured lower LC‐excess in rainfall (−17.3‰) and spring water (−6.5‰), whereas wetter conditions resulted in greater values (rainfall = +17.5‰; spring water = +10.7‰). The lower and higher LC‐excess values in rainfall corresponded to the very strong 2014–2016 El Niño and 2018 La Niña, respectively. During the recent triple‐dip 2021–23 La Niña, LC‐excess exhibited a significant and consistently increasing trend. These findings highlight the importance of combining hydrometric, synoptic and isotopic monitoring as ENSO sentinels to advance our current understanding of ENSO impacts on hydrological systems across the humid Tropics. Such information is critical to constraining the 21st century projections of future water stress across this fragile region.