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Regime shifts in benthic invertebrates within coastal ecosystems threaten the survival of wading birds (Charadrii). Predicting how invertebrate regime shifts will affect wading birds allows conservation management and mitigation measures to be implemented, including protection of terrestrial feeding areas. An individual-based model was used to investigate the impact of regime shifts on wading birds through their prey (marine worms and bivalves) in the estuarine system Poole Harbour, (UK). The model predicted the number of curlew (Numenius arquata), oystercatcher (Haematopus ostralegus), black-tailed godwit (Limosa limosa), redshank (Tringa totanus) and dunlin (Calidris alpina) supported in the Harbour during the non-breeding season (autumn and winter months). The most dramatic declines in bird numbers were for regime shifts that reduced the abundance of the largest invertebrates, particularly marine worms. The least adaptable bird species (those with the most restrictive diets) were unable to compensate by consuming other prey. Generally, as birds adapt to changes by switching to alternative prey species and size classes, changes in invertebrate size and species distribution do not necessarily affect the number of birds that the Harbour can support. Our predictions reveal a weakness in using birds as indicators of site health and invertebrate regime shifts. Differences in bird populations would not necessarily be detected by standard survey methods until extreme changes in invertebrate communities had occurred, potentially beyond the point at which these changes could be reversed. Therefore, population size of wading birds should not be used in isolation when assessing the conservation status of coastal sites.