Threats included reservoir construction, hydroelectric dams, and irrigation schemes.

The rufous-throated dipper was described by the German ornithologist Jean Cabanis in 1882 and given the binomial name Cinclus schulzii.

[3] The type locality is the mountain of Cerro Bayo in northern Argentina.

[4] The specific epithet schulzii was chosen to honour the German zoologist Friedrich W. Schulz (1866-1933) who had collected the specimen.

[6] Of the five species now placed in the genus, a molecular genetic study has shown that the rufous-throated dipper is most closely related to the other South American species, the white-capped dipper (Cinclus leucocephalus).