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Abstract The impacts of El Niño‐Southern Oscillation (ENSO) on salinity and alkalinity in an equatorial coral reef lagoon (Kanton) are investigated using water samples collected in three non‐El Niño years (1973, 2012, and 2018) and one El Niño year (2015). A one‐dimensional, advective‐diffusive model is developed to aid in the interpretation of the sparse observations and make estimates of net ecosystem calcification (NEC) rates. The Kanton lagoon experiences extreme salinity and alkalinity variations driven by ENSO variations in precipitation. During the non‐El Niño years, salinity increases from the ocean (35.5 psu) to the back of the lagoon (38 psu) because evaporation exceeds precipitation, and water resides in the back of the lagoon for ∼180 days. Early in the 2015–2016 El Niño, the back of the lagoon is only ∼1 psu saltier than the ocean because precipitation had begun to exceed evaporation. The model suggests that during El Niño events, when precipitation substantially exceeds evaporation, the back of the lagoon is less salty than the ocean (30–32 psu). Alkalinity variations in the lagoon are primarily due to dilution or concentration driven by the ENSO variations in precipitation and NEC that causes an alkalinity deficit of ∼250 μmol/kg in the back of the lagoon. The estimated NEC rate in 2015 is ∼25% lower (4.1 mmol/day) than in the non‐El Niño years (5.3–5. 7 mmol/day). The NEC rates and coral cover measurements indicate that the Kanton lagoon has recovered from the complete loss of coral cover during the 2002–2003 El Niño.