Salinity tolerances of reef corals have been experimentally investigated since the early twentieth century. Yet, nearly 100 years later, we are no closer to having a threshold that can be applied in studies of the impacts of freshwater runoff on coral communities. We present an empirically derived salinity threshold for sensitive Acropora species from the Keppel Islands in the southern inshore Great Barrier Reef (GBR), based on in situ salinity exposure and coral responses during a major flood event in 2010–2011. This threshold is presented as a dose-time response for a salinity-sensitive range of 22–28 PSU and an exposure time of 3–16 days at the lowest and highest salinities, respectively. The robustness of the salinity threshold was confirmed by comparison with responses of corals to low salinity 600 km north in the central GBR, which were exposed to substantially different turbidity and chlorophyll levels during the period of hypo-salinity.