There is a widespread concern about the direct and indirect effects of industrial fisheries; this concern is particularly pertinent for so-called “marine protected areas” (MPAs), which should be safeguarded by national and international law. The intertidal flats of the Dutch Wadden Sea are a State Nature Monument and are protected under the Ramsar convention and the European Union's Habitat and Birds Directives. Until 2004, the Dutch government granted permission for ~75% of the intertidal flats to be exploited by mechanical dredgers for edible cockles (Cerastoderma edule). Here we show that dredged areas belonged to the limited area of intertidal flats that were of sufficient quality for red knots (Calidris canutus islandica), a long-distance migrant molluscivore specialist, to feed. Dredging led to relatively lower settlement rates of cockles and also reduced their quality (ratio of flesh to shell). From 1998 to 2002, red knots increased gizzard mass to compensate for a gradual loss in shellfish quality, but this compensation was not sufficient and led to decreases in local survival. Therefore, the gradual destruction of the necessary intertidal resources explains both the loss of red knots from the Dutch Wadden Sea and the decline of the European wintering population. This study shows that MPAs that do not provide adequate protection from fishing may fail in their conservation objectives.