Seagrass ecosystems provide unique coastal habitats critical to the life cycle of many species. Seagrasses are a major store of organic carbon. While seagrasses are globally threatened and in decline, in Cairns Harbour, Queensland, on the tropical east coast of Australia, they have flourished. We assessed seagrass distribution in Cairns Harbour between 1953 and 2012 from historical aerial photographs, Google map satellite images, existing reports and our own surveys of their distribution. Seasonal seagrass physiology was assessed through gross primary production, respiration and photosynthetic characteristics of three seagrass species, Cymodocea serrulata, Thalassia hemprichii and Zostera muelleri. At the higher water temperatures of summer, respiration rates increased in all three species, as did their maximum rates of photosynthesis. All three seagrasses achieved maximum rates of photosynthesis at low tide and when they were exposed. For nearly six decades there was little change in seagrass distribution in Cairns Harbour. This was most likely because the seagrasses were able to achieve sufficient light for growth during intertidal and low tide periods. With historical data of seagrass distribution and measures of species production and respiration, could seagrass survival in a changing climate be predicted? Based on physiology, our results predicted the continued maintenance of the Cairns Harbour seagrasses, although one species was more susceptible to thermal disturbance. However, in 2011 an unforeseen episodic disturbance - Tropical Cyclone Yasi - and associated floods lead to the complete and catastrophic loss of all the seagrasses in Cairns Harbour.