Its natural habitats are subtropical or tropical moist lowland forests and freshwater springs.

Synapturanus salseri are shy and spend almost all of their time in burrows beneath the forest floor.

The frog was originally discovered by William F. Pyburn (former head of the biology department of the University of Texas at Arlington) and J. K. Salser Jr., an amateur biologist.

While collecting specimens in the Colombian rain forest near the village of Timbo on the Vaupes River, Pyburn heard the frog call.

After the leaf litter on the forest floor had been removed it became apparent that the frog was underground and it was captured after a careful excavation.