Gorgona National Natural Park (GNNP), in the Colombian Pacific Basin, harbors the most developed Pocillopora-dominated fringing reefs of the Tropical Eastern Pacific (TEP). These reefs experience upwelling bringing high pCO₂, total alkalinity (TA) and dissolved inorganic carbon (DIC), and low pHₜ and aragonite saturation (Ωarag) to the surface, and extreme riverine forcing from over 200 rivers, whose low-pHₜ, low-TA plumes couple land to reef chemistry. We present the first full annual cycle of monthly in situ carbonate monitoring (September 2021–October 2022) at seven stations (2–80 m) along a coastal–oceanic gradient, spanning all three climatological phases, plus 24-hour in situ incubations (n = 8) of Pocillopora spp. fragments (calcification from TA anomalies). Mixing models separated physical from biological drivers.

During a strong La Niña, physical mixing explained >90% of DIC and TA variability, driving an acidification "pincer effect": warm, low-salinity plumes diluted surface TA (down to 1858 µmol kg⁻¹), DIC and pCO₂ from above, while cold upwelled waters supplied high pCO₂ (up to 1088 µatm) and alkalinity from below, raising the Revelle factor to 10.48 ± 1.34 (pHₜ down to 7.63; Ωarag down to 1.87). Pre-upwelling, under terrestrial dominance, was the most diluted yet most favorable: lowest TA, DIC and pCO₂, but highest pHₜ (8.05 ± 0.04) and Ωarag (2.90 ± 0.26). Upwelling inverted this state (pHₜ 7.98 ± 0.11), as upwelled water enriches TA and DIC but acidifies the surface. Post-upwelling was warmest (27.16 ± 1.16 °C), with intermediate pCO₂ and Ωarag spanning annual extremes (1.56–3.57). GNNP is distinguished by amplitude, not mean state, rivaling eastern boundary upwelling systems.

The incubations exposed a biomineralization paradox. Fragments in deep (80 m), cold (19.65 °C), CO₂-rich (903 ± 175 µatm) and corrosive water (pHₜ 7.73; Ωarag 1.79), yet alkalinity-rich and weakly buffered, calcified 1.7-fold faster (2.049 mmol m⁻² h⁻¹) than fragments in warm, apparently favorable surface water (pHₜ 8.30; Ωarag 4.22), alkalinity-depleted and rigidly buffered. The paradox resolves in the ionic matrix, not bulk thermodynamics: weak buffering lets symbiont photosynthesis elevate local pHₜ and Ωarag, sustaining calcification despite hostile bulk conditions. TA, DIC, pCO₂ and Revelle factor peak during upwelling, pHₜ and Ωarag during pre-upwelling; post-upwelling is defined by variability, not means. Acidification at GNNP reflects terrestrial disruption of the ionic balance: alkalinity and the carbonate-ion pool, not pHₜ or Ωarag alone, limit calcification. This first annual baseline supports SDG 14.3.1 monitoring and adaptive management of TEP reefs amid intensifying land–ocean coupling.

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