Worldwide, local extinctions and severe declines in waterbird densities are being reported from many important waterbird sites. Waterbird sites often exist as a network, collectively providing crucial habitat for different life history stages of different species. Therefore, population changes at one site may strongly influence others. In Australia, many waterbird species are highly mobile, and move rapidly over long distances in response to rainfall. Large tidal wetlands often serve as drought refugia or alternative breeding habitat for these species. These sites are also the migration terminus of many species of shorebirds that spend their non‐breeding season in Australia. One such site in south‐eastern Australia is Western Port, a Ramsar‐listed tidal embayment forming part of the East Asian–Australasian Shorebird Site Network. We measured waterbird population trends over nearly 40 years in Western Port to see whether changes showed consistent trends over time across multiple species. Thirty‐nine species were recorded often enough to allow an analysis of trends over time using dynamic linear models and, where appropriate, piecewise linear regression. Twenty‐two species had declined, including four species of duck, five species of fish‐eating bird (cormorants, terns and pelicans), one species each of grebe, gull and heron, and 10 species of shorebird. Only two species (Australian pied oystercatcher Haematopus longirostris and straw‐necked ibis Threskiornis spinicollis) increased significantly over the same time period. Patterns of decline in non‐migratory waterbirds may reflect diminishing wetland availability, local reductions in fish prey, increased predation pressure and changes in inland wetland resources. Declines in migratory shorebirds are most likely related to loss of habitat elsewhere in their trans‐equatorial migration routes. These trends in waterbirds that use Western Port reflect widespread impacts on populations elsewhere in Australia and overseas, necessitating more than simply local management of this tidal embayment.