Generally marine seagrass specialists, they inhabited the warm and shallow waters of the Paratethys, Mediterranean, Caribbean Sea and Pacific coastline.

American species of Metaxytherium are considered to be ancestral to the North Pacific family Hydrodamalinae, which includes the giant Steller's sea cow.

[4] While M. krahuletzi and M. medium go through only relatively slight morphological changes, M. serresii represents a strange diversion from the overall trend observed among the European Metaxytherium chronospecies.

Originally, Domning and Thomas suggested that this drastic reduction in body size may have been a direct result of the Messinian salinity crisis, creating suboptimal conditions for the European seagrass fields and in turn affecting the sirenian population until the plant life could recover.

[24] The drastic increase in tusk size would also support this hypothesis, suggesting that when faced with declining resources, the European Metaxytherium adapted to better exploit what was available, including the rhizomes of seagrasses.

Despite its adaptations to the cooling climate, Metaxytherium subapenninum failed to change its seagrass based diet in the same way the hydrodamalines of the Bering Sea did, eventually dying out towards the end of the Pliocene as temperatures continued to drop.

[25][23] The presence of Metaxytherium species on the western coast of the Americas, in addition to their close phylogenetic ties with the Hydrodamalinae, has been suggested to represent a second anagenetic lineage starting with M. crataegense entering Peru via the Central American Seaway.

The hypothesis also suggests that this northern lineage would further give rise to Dusisiren and eventually culminate in the algae specialist Hydrodamalis, which persisted until historic times.

In modern taxa, dugongs show a sharply downturned upper jaw, generally associated with its grazing lifestyle, while manatees have comparably shallow rostral deflection.

Although not thoroughly researched, it's hypothesized that the downturned snout helps with grazing by keeping the mouth close to the ground while maintaining a horizontal posture for the rest of the body.

Both types of skull morphology can be seen in the two analyzed taxa, with M. crataegense having a relatively straight upper jaw while M. floridanum shows a strong downturn similar to the dugong.

As conditions in the Mediterranean stabilized, previously dominant seagrasses such as Posidonia oceanica recolonized the area and become a key component in the sirenian's diet.

M. subapenninum could have developed its larger tusks to specifically feed on the thick and nutrient rich rhizomes of Posidonia rather than returning to their previous diet.

Although not particularly complete, the fossil proved to be significant as it was preserved alongside seven teeth belonging to the extinct tiger shark Galeocerdo aduncus.

[28] Another paper from the same year describes fossils of M. subapenninum that bear toothmarks similar to those of extant juvenile Bluntnose sixgill sharks.