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We analysed standardised estimates of local occupancy probability of 13 species of native wading birds, terns and gulls (order Charadriiformes) derived from the New Zealand Ornithological Society’s national Atlas of Bird Distribution collated in 1969–1979 and 1999–2004. We show systematic patterns in changes with taxonomic level of endemism, breeding habitat (coastal or inland), and location (distance from the coast, road density, and degree of land development for agriculture and forestry). The main changes were decreases in endemic inland breeding species within their inland South Island breeding ranges, and increases in most coastal-breeding species and some inland-breeding species around much of the coast, especially near urban centres in the North Island. Our results are consistent with both intensive land use and predation contributing to widespread declines of inland-breeding species across inland South Island. Potential causes of occupancy changes around the coast are less clear, and we offer some suggestions.