Automated cavity ring down spectroscopy was used to make continuous measurements of dissolved methane, nitrous oxide, and carbon dioxide in a coral reef lagoon for 2 weeks (Heron Island, Great Barrier Reef). Radon (222Rn) was used to trace the influence of tidally driven pore water exchange on greenhouse gas dynamics. Clear tidal variation was observed for CH4, which correlated to 222Rn in lagoon waters. N2O correlated to 222Rn during the day only, which appears to be a response to coupled nitrification-denitrification in oxic sediments, fueled by nitrate derived from bird guano. The lagoon was a net source of CH4 and N2O to the atmosphere and a sink for atmospheric CO2. The estimated pore water-derived CH4 and N2O fluxes were 3.2-fold and 24.0-fold greater than the fluxes to the atmosphere. Overall, pore water and/or groundwater exchange were the only important sources of CH4 and major controls of N2O in the coral reef lagoon.