Satellite-based ocean remote sensing is fundamentally limited to observing the ocean surface (top-of-the-ocean), a constraint that severely hinders a comprehensive understanding of how the entire water column ecosystem responds to climate variability like the El Niño-Southern Oscillation (ENSO). Surface-only views cannot resolve critical shifts in the subsurface chlorophyll maximum (SCM), a key layer for marine biodiversity and biogeochemical cycles. To overcome this critical limitation, we develop and validate a novel stacked generalization ensemble machine learning framework. This framework robustly reconstructs a 25-year (1998–2022) high-resolution 3D chlorophyll-a (Chl-a) field by integrating 133,792 globally distributed Biogeochemical-Argo (BGC-Argo) profiles with multi-source satellite data. The reconstructed 3D Chl-a fields were rigorously validated against both satellite and in-situ observations, achieving strong agreement (R ≥ 0.97, mean absolute percentage error ≤ 27 %), demonstrating the robustness and reliability of the framework. Applying this framework to two contrasting South China Sea upwelling system reveals that ENSO phases fundamentally restructure the entire water column. Crucially, we discover that El Niño and La Niña exert opposing effects on the SCM: El Niño events deepen and thin the SCM with decreasing Chl-a by 15–30 %, whereas La Niña events cause it to shoal and thicken, increasing Chl-a by 20–40 %. This vertical restructuring is mechanistically linked to ENSO-driven changes in wind stress curl, Rossby wave propagation, and nitrate availability. Furthermore, we identify a significant subsurface-first response, where the SCM reacts to ENSO forcing months before significant changes are detectable at the surface. Our findings demonstrate that a three-dimensional perspective, enabled by our novel remote sensing reconstruction framework, is essential for accurately quantifying the biogeochemical consequences of climate variability, revealing that surface-only observations can significantly underestimate the vulnerability and response of marine ecosystems to ENSO events.
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