William may have been a son of Henry Abernethy and a nephew of Hugh Abernethy. William acquired Saltoun (ELO) and Oxton in Lauderdale, or at least some rights there, through the connections with the Galloway constables and lords of Lauderdale. Hugh and probably Henry were sons of Laurence Abernethy, whose wife Dervorguilla was almost certainly Alan of Galloway's aunt. William made a donation to Dryburgh Abbey in 1273 and may have died soon thereafter. William was married to a woman named Margaret, who was a widow in 1296.
Fordun and Wyntoun claimed that William Abernethy was involved in the 1289 murder of Earl Duncan of Fife, but this was almost certainly a mistake for Hugh, who was imprisoned for the crime.