Due to severe fluctuations in water levels and chemical composition, this species is mostly restricted to the margins of the lake in spring fields of varying salinity.

These ponds are typically very shallow and occupied by growths of filamentous algae of the genus Chara.

Winter rainfall allows migration between sites through rivulets around the periphery of the lake, causing a greater genetic diversity within populations, which extend across 1 km2 (0.39 sq mi).

[2][3] Aphanius transgrediens occupies an extremely restricted area of 30 springs that is almost entirely in danger of destruction by the construction of a new road.

In addition, A. transgrediens is threatened by invasive species, degradation of habitat (also by livestock trampling), and climate change.