Persisting at the edge of ecological collapse: the impact of urbanization on fish and amphibian communities from Lake Xochimilco

Freshwater ecosystems are globally threatened by habitat loss, pollution, and invasive species, all of which are particularly acute in urban areas. To assess the impacts of urbanization on freshwater biodiversity—specifically the effects of alien species on native primary aquatic vertebrates—we investigated the World Heritage Site, Lake Xochimilco in Mexico City. Focusing on fishes and amphibians, we applied environmental DNA metabarcoding using primer pairs targeting mitochondrial 12S and 16S across the remnant lake and collected 14 aquatic environmental variables for sampled sites. Our survey recovered ca. 60% of Lake Xochimilco's historically recorded fish and amphibian species, including rare species and novel taxa not detected by past traditional surveys. However, our findings imply a severely degraded wetland, with alpha diversity indices indicating a low‐diversity ecosystem dominated by alien fishes. Beta diversity analysis revealed a heterogeneous ecosystem that may be driven partially by the presence of alien fish, particularly cyprinids. Environmental variables linked to pollution predicted the presence of non‐native fish families. We also found evidence that some species prefer to occupy different water bodies within the lake remnant. Despite the ongoing degradation of this ecosystem, native and endemic fauna are persisting, although detections were typically rare. We found no evidence of the Critically Endangered axolotl salamanders (<jats:italic>Ambystoma</jats:italic> sp.) from wild sites; however, we detected their presence in one wildlife refuge, highlighting the potential of refuges to prevent complete extinction in the wild. We also found evidence of cryptic taxonomic diversity in <jats:italic>Lithobates</jats:italic> frogs and evidence of endemic genera, including the threatened mexclapique fish (<jats:italic>Girardinicthys viviparus</jats:italic>). These fishes are considered extirpated, suggesting remnant populations persist undetected by traditional surveys. Despite clear evidence of an ecosystem under extreme decline compared to historical biological records, our study demonstrates the potential for restoration, given the presence of native freshwater species and the success of wildlife refuges.