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Fisheries and other human activities pose a global threat to the marine environment. Marine protected areas (MPAs) are an emerging tool to cope with such threats. In the Dutch Wadden Sea, large MPAs (covering 31% of all intertidal flats) have been created to protect shellfish-eating birds and allow recovery of important habitats. Even though shellfish fishing is prohibited in these areas, populations of shellfish-eating birds in the Wadden Sea have declined sharply. The role of shellfish fisheries in these declines is hotly debated, therefore, we investigated the effectiveness of MPAs for protecting oystercatcher (Haematopus ostralegus) populations. Shellfish stocks (cockles, Cerastoderma edule) were substantially higher in the MPAs, but surprisingly this has not resulted in a redistribution of wintering oystercatchers. Oystercatchers in unprotected areas had less shellfish in their diet and lower condition (a combined measure of mass and haematological parameters), and their estimated mortality was 43% higher. It is likely, therefore, that shellfish fishing explains at least part of the 40% decline in oystercatcher numbers in recent years. Condition and mortality effects were strongest in males, and the population sex ratio was female biased, in agreement with the fact that males rely more on shellfish. The unprotected areas apparently function as an "ecological trap," because oystercatchers did not respond as anticipated to the artificial spatial heterogeneity in food supply. Consequently, the MPAs are effective on a local scale, but not on a global scale. Similar problems are likely to exist in terrestrial ecosystems, and distribution strategies of target species need to be considered when designing terrestrial and marine protected areas if they are to be effective.