In North America, it is found along the Atlantic Coast from Nova Scotia to the Boston Harbor islands, where its presence in low-pollution areas indicates its potential as a bioindicator for marine lichen community health, and on the west coast in British Columbia, particularly in the Gwaii Haanas's upper littoral fringe.

The lichen was originally described in 1807 by the Spanish botanist Simón de Roxas Clemente y Rubio, who classified it as a species of Verrucaria.

His Latin description of the organism was brief: Crusta subtartarea suborbiculari uniformi contigua aequabili picea nitida, tuberculis subcylindricis tandem subpatellulaeformibus ('The crust is almost tartarean, suborbicular, uniform, contiguous, even, pitch-black, shiny, with tubercles initially subcylindrical then eventually somewhat in the form of a small patella (kneecap)').

[3][note 1] In 2011, Claude Roux reclassified the taxon to Hydropunctaria,[4] a genus previously branched out from Verrucaria in 2009 to form its own distinct group.

[6] The crustose lichen Hydropunctaria amphibia is characterised by a prothallus that is typically inconspicuous, but in some specific, small areas, it can become visible as a whitish layer.

[7] The photobiont of H. amphibia specimens collected in the Iberian Peninsula was Halofilum ramosum (a species of green alga in the order Ulvales).

[11] Another source suggests that when wet, H. amphibia becomes more light coloured and translucent compared to H. maura, and so its ridges become more distinctly contrasted.

[8] In comparison, Wahlenbergiella striatula, another marine lichen species that may present ridges on its thallus, differs primarily in the size of its ascospores, which are smaller than those of Hydropunctaria amphibia.

In the latter location, it only grows in low-pollution areas, suggesting low pollution tolerance, and potential for use as a bioindicator of marine lichen community health.