Banjo, the five-year-old Staffordshire Bull Terrier, was at Dripstone Cliffs, Casuarina, playing in knee-deep water on the beach at around 9am, when he was bitten on the backside.
Banjo’s owner said he was surprised his dog went for another swim after the attack.
He was taken to the vet and treated for three bite marks on his back, but didn’t need stitches.
Banjo is now recovering and resting back at home.
Wildlife authorities have set traps in the Casuarina area in an effort to locate the crocodile.
Crocodile sightings in Darwin are extremely common, with residents warned to be aware of them when in coastal areas.