High-resolution measurements of Sr/Ca and 18O/16O in mid-Holocene and modern Porites corals were used to derive a history of freshwater fluxes to the Australian Great Barrier Reef (GBR). Interannual variations in dry-season seawater 18O/16O evident in the coral record for the late 20th century, but not 6200 years ago, correlate with variations in groundwater recharge of coastal aquifers. The results suggest that a delay in groundwater recharge following the post-glacial sea-level rise, and recent deforestation for agriculture, may have lead to higher land-sea hydraulic gradients and greater groundwater discharge to the GBR today. Oxygen-isotope mass balance calculations show that ∼3% in-mixing of CO2-enriched groundwater could raise the partial pressure of CO2 in coastal seawater by ∼90 μatm following strong summer monsoons. Consequently, modern nearshore corals in the GBR may now be subjected to lower aragonite saturation states, which could reduce coral calcification and contribute to recent reef degradation.