Migratory shorebirds are declining in all transequatorial flyways, most rapidly in the East Asian–Australasian Flyway. Population trends for shorebirds have been derived at a flyway and continental scale, but changes at the local scale are less well understood. Here we compare trends in migratory shorebird populations using natural and artificial roost sites within a tropical harbour, examine possible drivers of change, and identify appropriate conservation management responses. Counts of 19 migratory shorebird species from 2010 and 2018 showed that total abundance increased at an average annual rate of 3.3% (95% CI = 1.3–5.4%, P = 0.001) across five natural roost sites. This was driven largely by increases in great knot, with most other species declining. At an artificial site in an adjacent shorebird area, total abundance increased at an average annual rate of 14.5% (95% CI = 10.5–18.6%, P ≤ 0.000), with few species declining. These results suggest that there is a need to include both natural and artificial sites within shorebird conservation and management planning and that trends in different species can be driven by a combination of local and external drivers.