Facultative paedomorphosis, a process in which newt larvae can opt for reproduction before or after metamorphosis, is geographically heterogeneous. Despite numerous ecological studies and recent evidence of declines in paedomorphic populations, however, no attempt to model environmental variables that explain the presence of paedomorphs has been made at a multi-scale level. Our aim was to fill this gap in studying three newt species ( Lissotriton vulgaris, Mesotriton alpestris, and Triturus macedonicus) of the Montenegrin karst as model species. To this end, we used multivariate analysis on three scales of habitat: the breeding pond, the land use and the climatologic features. Results show that the study area is both an important hotspot for paedomorphosis and where intraspecific diversity is quickly disappearing (20–47% extirpation) because of fish introductions. Other habitat variables (water permanency, pH or the habitat origin) were shown to act on paedomorphosis but not consistently across species, confirming complexity of the evolutionary and ecological processes. This study appeals for more long-term and detailed landscape studies of polyphenisms, a neglected but promising topic, to better understand and protect alternative modes of development. Particularly, measures should be taken to identify hotspots of intraspecific diversity at a global scale and stop fish introductions before we reach a point of no-return.