The original diversity of Pelophylax water frogs has been compromised by multiple biological invasions all over Western Europe. For the European pool frog (P. lessonae), the Joux Valley—a 30 km highland depression in northwestern Switzerland—stands as the last stronghold spared by exotic lineages. In order to manage P. lessonae in the valley, we combined traditional field surveys with environmental DNA metabarcoding and mapped the regional distribution of amphibian species. Both approaches concurred that P. lessonae persists at a single isolated site (Pontet). Continuous monitoring of this population throughout the spring and summer 2019 informed on their wintering quarters (most likely the forest litter immediately surrounding the breeding pond), as well as the timing of migration (end of April), breeding (June), and larval development (June–August). In parallel, we experimented the first use of drone technology for amphibian surveillance: 30 adults were individually counted during an aerial survey at the peak of the breeding season, confirming the small size of the population. Finally, we compared some biotic and abiotic properties among water bodies throughout the valley and flagged a few sites that were ecologically similar to Pontet. In a landscape dominated by pastoral activities where Pelophylax dispersal is virtually impossible, these could be candidates for future translocation efforts. Our study illustrates the application of next-generation monitoring techniques for the urgent management of threatened species and stresses the need for reevaluating the conservation status of P. lessonae in Western Europe, where it appears to subsist in low numbers at one last locality.