While most studies assessing the ecological impacts of climate change have examined impacts from warming temperatures, less attention has been given to other parameters such as increased rainfall events. At a nesting rookery in the northern Great Barrier Reef, Australia, we used data loggers to examine the impact of heavy rainfall and shade on the nest temperatures for green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) turtles clutches, which have temperature-dependent sex determination. In the middle of the nesting season (December–March), on 21 January 2019, 125 mm of rain fell over two days, causing the temperature to initially decrease by an average of ~ 3.6 °C in hawksbill turtle nests (n = 18) and ~ 3.5 °C in green turtle nests (n = 9). For shaded clutches during the 20-day cooling period after the rainfall event, we report average nest temperatures of ~ 27.9 °C and ~ 28.2 °C for hawksbill and green turtle clutches respectively, falling well into the male-producing range for sex determination. This was profoundly cooler than the average nest temperatures of clutches without shade and prior to the heavy rainfall, which was ~ 31.3 °C for both species. Extreme rainfall events are predicted to increase around Australia due to climate change but may help counteract impacts of atmospheric warming on sea turtle offspring sex-ratios. Our results also show the potential for artificially cooling nests by applying a combination of shade and irrigation, to counter the expected increases in the feminisation of sea turtle hatchling production worldwide.