Water Isotopes Reveal How El Niño Reshaped Amazon Rainfall

The catastrophic droughts that gripped the Amazon in 2023 and 2024 did more than shrink rivers and strand communities across the world’s largest rainforest. They also left a subtle chemical signature in every raindrop that fell over the region, a signature that Brazilian scientists have now learned to read. By monitoring the isotopic composition of daily rainfall in Manaus, the capital of the Brazilian state of Amazonas, researchers at São Paulo State University (UNESP) have shown that water molecules carry a kind of fingerprint of where their moisture came from and what atmospheric conditions shaped their journey. That fingerprint, they argue, could serve as an early warning system for the prolonged droughts that climate change is making increasingly frequent and severe in the Amazon basin.

The study, led by geographer Rafaela Rodrigues Gomes, a doctoral candidate at UNESP’s Institute of Geosciences and Exact Sciences in Rio Claro, and coordinated by geologist Didier Gastmans, head of the university’s Laboratory of Water Resources and Environmental Isotopes, is among the first in more than three decades to apply isotopic techniques to Amazonian hydroclimatic research. Published in June in the journal Hydrological Processes and based on Gomes’s master’s thesis, the work was supported by the São Paulo Research Foundation (FAPESP). Its central premise is elegantly simple: because water molecules containing heavier isotopes behave slightly differently from those containing lighter ones, the ratios between them record the history of evaporation and condensation that each parcel of rain has undergone.

Isotopes are lighter or heavier versions of atoms of the same chemical element, distinguished by the number of neutrons in their nuclei. Water is composed of hydrogen and oxygen, and while most hydrogen nuclei contain just a single proton, a small fraction carry a neutron as well, making them roughly twice as heavy. Oxygen shows similar variation, with most nuclei holding eight neutrons but some carrying nine or ten. These differences matter because lighter water molecules evaporate more readily, while heavier molecules condense first. As Gomes explains, the ratios between light and heavy isotopes are continuously altered by evaporation and condensation throughout the hydrological cycle. Each combination of temperature, humidity and other meteorological variables produces a distinct isotopic profile, which is why researchers describe the measurements as a water fingerprint.

The new study revives a scientific tradition with deep roots in Brazil. Research on rainfall isotope variation in the Central Amazon began in the 1960s, driven primarily by scientists at the Center for Nuclear Energy in Agriculture at the University of São Paulo in partnership with the International Atomic Energy Agency. Between 1965 and 1990, monthly rainwater samples were collected in Manaus, though with interruptions in some years, before a lack of funding ended the program entirely. Only in 2020, thanks to a collaboration involving UNESP, the National Institute for Amazonian Research (INPA), the Geological Survey of Brazil and other institutions, did a new monitoring network begin to take shape in the region, with part of its funding provided through a project jointly financed by the Amazonas State Research Foundation and FAPESP.

For the current study, INPA researchers collected 207 daily rain samples in Manaus between March 2023 and February 2025, a period that happened to span two of the most extreme drought years in the Amazon’s recorded history. The samples were divided among three laboratories for analysis: UNESP’s Laboratory of Water Resources and Environmental Isotopes in Rio Claro, the Center for Stable Isotopes at UNESP’s Botucatu campus, and the Tracer Hydrology Group at the University of Texas at Arlington in the United States. To interpret the isotopic data, Gomes compared it with measurements from a weather station installed beside the rain collector and cross-referenced the results with global meteorological data and models from the European Centre for Medium-Range Weather Forecasts and the U.S. National Oceanic and Atmospheric Administration.

The analysis revealed a clear seasonal choreography of atmospheric systems. During the rainy months of March, April and May, the Intertropical Convergence Zone, a broad band of clouds encircling the Earth near the equator that is responsible for roughly 30 percent of the planet’s precipitation, dominates the isotopic record. In this period the convergence zone shifts southward, drawing in moist air masses from the North Atlantic. As these air masses travel from the ocean toward Manaus, they release successive episodes of rain, and each successive rainfall event enriches the remaining vapor’s proportion of light isotopes. From June to August, the convergence zone retreats northward and drier weather settles over the Amazon. The study showed that during this dry season the proportion of heavy isotopes rises again, a shift controlled by a different atmospheric player: the South Atlantic Subtropical High, a high-pressure system that steers drier air masses into the region and suppresses rainfall.

In the months that follow, moisture arrives from both the northern and southern Atlantic, and isotopic variation becomes governed mainly by local conditions such as rainfall volume rather than by large-scale circulation systems. The physics of this local control is intuitive once broken down. Water from weak rainfall events contains more heavy isotopes because the heavier molecules are the first to condense and fall. Intense storms, by contrast, dilute the concentration of heavy isotopes in the downpour. The famously humid Amazonian air also suppresses evaporation, which would otherwise strip light isotopes from falling raindrops, while the rapid evaporation-condensation cycling inside summer thunderstorms concentrates heavy isotopes. The net effect is that isotopic values swing widely at this time of year, reflecting the interplay of storm intensity, humidity and temperature in ways that monthly sampling would blur beyond recognition.

That last point underscores the study’s key methodological innovation. Research from the 1970s and 1990s had already suggested that the Intertropical Convergence Zone and local meteorological conditions influenced rain isotopes in Manaus, but the technology of the era and the monthly sampling frequency, which mixes many atmospheric processes into a single averaged sample, prevented finer distinctions. Daily monitoring changed that. For the first time, Gomes was able to separate not only the convergence zone’s influence but also, for the first time in the Amazonian record, the contribution of the South Atlantic Subtropical High. When she compared the new data with the measurements collected between 1965 and 1990, she found clear changes in isotopic composition, changes linked to today’s warmer and drier conditions. The Amazon, after all, suffered its worst heat waves and prolonged droughts since 1902 during 2023 and 2024.

The drivers of those extreme events are well understood in broad outline. Above-average warming of Pacific surface waters, the phenomenon known as El Niño, occurs naturally every two to seven years and disrupts wind and rainfall patterns worldwide, and global warming has increased the frequency of its most extreme manifestations. In the Central Amazon, El Niño promotes the sinking of moist air, hindering cloud formation. In 2023 and 2024 this effect combined with abnormal warming of the North Atlantic, which pushes the Intertropical Convergence Zone further north and cuts off the inflow of moisture into the basin. The isotopic record captured the consequences directly: raindrops evaporating in warmer, drier air concentrate heavier isotopes, and the isotopic signature typical of the dry season appeared earlier than usual. In 2024, when the drought proved even worse than the previous year’s, that signal emerged in May rather than its historical June arrival.

That early appearance is precisely what makes the technique promising as a drought early warning. The researchers wrote in their article that the finding reinforces the potential of stable isotopes as early warning indicators for prolonged droughts, especially in a changing climate. Gastmans describes it as another easy-to-obtain, relatively low-cost indicator, while cautioning that confirming the signal’s reliability will require much longer observational records, on the order of 20 to 30 years for hydrological phenomena. The effort is already expanding. In doctoral research begun in February and funded by the Coordination for the Improvement of Higher Education Personnel, Gomes is collecting rain samples at 19 stations across the Amazon and neighboring regions, aiming to trace the origins of Atlantic water vapor that recirculates through the forest, collides with the Andes and continues southward to feed Brazil’s Central-West, Southeast and South regions, the celebrated atmospheric conveyor known as the flying rivers. If the isotopic fingerprints hold their pattern, the rain itself may one day announce the droughts to come.

Subject of Research: Isotopic analysis of daily rainfall in the Central Amazon to track moisture sources and drought conditions

Article Title: Scientists use water isotopes to map changes in Amazon rainfall

Article References: Scientists use water isotopes to map changes in Amazon rainfall. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: Amazon rainforest, water isotopes, El Niño, drought, Intertropical Convergence Zone, hydroclimate, Manaus, flying rivers, climate change, rainfall monitoring, South Atlantic Subtropical High, UNESP