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 1973, 2012, 2015, and 2018. A simple advective-diffusive model is developed to aid in the interpretation of the sparse observations and make estimates of net ecosystem calcification (NEC) rates. Salinity and alkalinity variations in Kanton lagoon are primarily driven by ENSO variations in precipitation. During non-El Niño years (1973, 2012, 2018), 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. At the onset of the 2015-16 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 Niños, when precipitation 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 micromoles/kg in the back of the lagoon. NEC rates in the early stages of the 2015 – 2016 El Niño were ~10% lower (4.7 mmol/day) than in the non-El Niño years (5.2 – 5. 5 mmol/day). The NEC rates and coral cover indicate that Kanton Lagoon has recovered from the complete loss of coral cover during the 2002-03 El Niño.