Springs along its length contribute to its flow. A series of wells accessing the river's groundwaters, drilled in the early 20th century, remained a major supply of potable water in the city into the late 20th century. The name of the river derives from the Lithuanian language word vilnis ("a surge") or vilnyti ("to surge").
Vilnelė, the diminutive form of the original hydronymVilnia, came into popular use in Lithuanian and largely replaced the latter.
In an effort to restore the upstream migration of salmonids in the basin, a fish ladder was constructed on the Vilnia in 2000.