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Protected area networks facilitate community changes in responses to climate warming. However, the contribution of the site environmental and conservation-oriented characteristics to these responses to climate warming are not well understood. Here, we investigate how composition of non-breeding waterbird communities within the European Union Natura 2000 (N2K) network changes in response to increases in temperature. We measured the community reshuffling of 97 waterbird species in 3,018 N2K sites over 25 years in 26 European countries. We find that N2K sites explicitly designated for protection of waterbirds and with a management plan had faster climate-driven community changes. In contrast, the designation period of the N2K sites was not associated with community adjustment, and sites funded under EU-LIFE had lower climate-driven community changes. Our findings imply that efficient conservation policy that may help waterbird community responses to climate warming is to manage sites that are specifically designated for waterbirds.