There are few studies of medium-term, quantitative changes in faunal communities in the southern hemisphere. The linear nature of coastlines makes populations of coastal birds easy to count. Repeat surveys of 278 km of coastline in three regions of the Western Cape, South Africa show marked differences in coastal bird community structure over the last 30 years, despite limited human impacts on coastal habitats (mainly increased human disturbance). The total number of birds has not changed, but species richness increased following colonization of the coast by Egyptian geese (Alopochen aegyptiaca, Anatidae) and three species of ibises (Threskiornithidae). Biomass also increased due to greater numbers of large-bodied birds. Contrary to the prediction that large birds are more susceptible to human disturbance, most small birds decreased in abundance. Among waders that breed along the coastline, numbers of African oystercatchers (Haematopus moquini, Haematopodidae) doubled, linked to increased food availability following invasions by alien mussels (Mytilidae). By comparison, numbers of white-fronted plovers (Charadrius marginatus, Charadriidae) decreased by 37% (59% close to Cape Town), at least in part as a result of increasing human disturbance. The greatest decreases occurred among migrant waders (Scolopacidae and Charadriidae), with numbers of the four most abundant species falling by >50%, and both common Calidris species by >90%. Migrant wader populations decreased in all three regions, irrespective of whether surveys were in protected areas or not, suggesting that factors outside the region are driving these trends. Some species may have decreased due to changes in their preferred wintering areas, but others probably reflect population decreases, confirming the generally poor conservation status of migrant waterbirds worldwide.