Organisms can be strongly affected by a range of natural and anthropogenic stressors in conjunction, making comprehensive assessments of multiple potential drivers of population dynamics essential. An 18-year dataset obtained for Michaelmas Cay in the northern Great Barrier Reef, Australia, was used to assess population trends for three tern species relative to two potential threatening processes, namely human impacts (as either commercial fishing or tourism) and cyclone activity. We found a positive, 2-year lagged relationship between long-line catch per unit effort in the Eastern Tuna and Billfish Fishery in the vicinity of Michaelmas Cay and breeding participation in the two pelagic foraging terns, but not in the inshore foraging tern. The abundance of large pelagic fish may influence recruitment into the breeding populations of the two pelagic terns in the following years through impacts on prey availability. Long-term population trends for all seabirds were not related to localised direct disturbance from cyclones or associated changes in cay size and/or nesting habitat. Current management protocols in place for the tourism industry at the cay appear to be minimising direct human impacts. Other evidence from this breeding location suggesting that climate variation may be driving foraging success and breeding-population dynamics in the two pelagic terns implies that a precautionary approach is warranted to the management of any potential stressors to birds in this system.