Gastropod-nematode associations are underreported worldwide. In the present study, juvenile and adult nematodes were found in the freshwater gastropod Burnupia stenochorias (Melvill & Ponsonby, 1903), from the Vaal River, South Africa. The nematodes were confirmed to belong to the genus Daubaylia chitwood & chitwood, 1934 (Daubayliidae). This is the first report of Daubaylia from a snail belonging to the family Burnupiidae, and the first report of this nematode taxon in southern Africa. Like D. pearsoni and D. malayanum from Australia and Malaysia respectively, adult females of the current species possess multiple well-developed eggs in the uteri, with larvae developing in utero. Morphological and molecular characteristics showed that the nematodes are distinct from all the described species of Daubaylia. Thus, they are considered a new species, Daubaylia burnupiae n. sp. The species differs from its congeners based on spicule shape, the short tail of the male, an anal cuticular knob-like protrusion on the female, and oesophagi with short isthmi and short glandular basal bulbs in both sexes. Three club-shaped pharyngeal lobes, extending slightly above the surface of the cephalic lips in both sexes and a pre-cloacal median papilla on the male were described using scanning electron microscopy, the first of such observations for the daubayliids. Genetic analyses showed that partial sequences of D. burnupiae n. sp. differed from species for which genetic data are available, by at least 26 and 9 base pair differences for 28S and 18S rDNA, respectively. Our results show that low prevalence and abundance of nematodes in the snails, corresponded with increased pollution in the river. We suspect that exposure to pollutants reduces the viability of the infective gravid female nematode during transmission. Therefore, the nematode is a potential bioindicator for aquatic pollution.