Abstract Protected areas (PAs) are crucial for biodiversity conservation, yet climate change threatens their long‐term effectiveness by displacing species distributions. Among the most climate‐threatened organisms are the amphibians, highly dependent on water and wetlands. The world's largest continuous tropical wetland, the Pantanal and surroundings, is situated in the Upper Paraguay River Basin (UPRB) in South America. Of the 74 amphibian species found there, 4% are threatened. Less than 5% of the basin is within PAs. Recurrent droughts and increasing human pressures further endanger the region's semiaquatic fauna if adequate protection measures are not implemented. Using Ensemble of Small Models, we mapped habitat suitability of amphibian species and projected amphibian richness and composition across the UPRB. We applied null models to evaluate the representation of amphibian ranges within the current PA network under both current and future climate scenarios. To prioritize areas for PA network expansion under climate change scenarios, we used a systematic conservation planning algorithm. By 2100, over 80% of amphibian species from the study area are projected to lose suitable habitat, with 99% of amphibian assemblages facing climate‐driven species loss. Although the existing PA network had limited species representation, protecting on average less than 5% of amphibian ranges. However, 13.7% of PAs are expected to shelter more amphibian species than expected by chance under future climate conditions. Highlands, particularly in the northern and southeastern boundaries of the UPRB, are identified priority areas for PA network expansion due to their high projected changes in amphibian biodiversity. Synthesis and applications. Our findings reveal the extensive impacts of climate change on a major semiaquatic group in the world's largest tropical wetland. Although the current PA network in the Pantanal and surroundings safeguards fewer amphibians than expected, its limited coverage provides opportunities for systematic, data‐driven expansion to achieve the Post‐2020 Global Biodiversity Framework's 30 by 30 target. Expanding PAs is urgent, but addressing drivers of environmental degradation, including unsustainable practices in agriculture and livestock farming, is equally critical for conserving this biodiverse ecosystem.
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