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Abstract Understanding the effects of intensification of Amazon basin hydrological cycling—manifest as increasingly frequent floods and droughts—on water and energy cycles of tropical forests is essential to meeting the challenge of predicting ecosystem responses to climate change, including forest “tipping points”. Here, we investigated the impacts of hydrological extremes on forest function using 12+ years of observations (between 2001–2020) of water and energy fluxes from eddy covariance, along with associated ecological dynamics from biometry, at the Tapajós National Forest. Measurements encompass the strong 2015–2016 El Niño drought and La Niña 2008–2009 wet events. We found that the forest responded strongly to El Niño‐Southern Oscillation (ENSO): Drought reduced water availability for evapotranspiration (ET) leading to large increases in sensible heat fluxes (H). PartitioningETby an approach that assumes transpiration (T) is proportional to photosynthesis, we found that water stress‐induced reductions in canopy conductance (G_s) droveTdeclines partly compensated by higher evaporation (E). By contrast, the abnormally wet La Niña period gave higherTand lowerE, with little change in seasonalET. Both El Niño‐Southern Oscillation (ENSO) events resulted in changes in forest structure, manifested as lower wet‐season leaf area index. However, only during El Niño 2015–2016, we observed a breakdown in the strong meteorological control of transpiration fluxes (via energy availability and atmospheric demand) because of slowing vegetation functions (via shutdown ofG_sand significant leaf shedding). Drought‐reducedTandG_s, higherHandE, amplified by feedbacks with higher temperatures and vapor pressure deficits, signaled that forest function had crossed a threshold, from which it recovered slowly, with delay, post‐drought. Identifying such tipping point onsets (beyond which future irreversible processes may occur) at local scale is crucial for predicting basin‐scale threshold‐crossing changes in forest energy and water cycling, leading to slow‐down in forest function, potentially resulting in Amazon forests shifting into alternate degraded states.