The man, 47, was wading across Cahill's Crossing near Kakadu National Park when he was taken by the 3.3m (11ft) reptile, police said.
Two women made it across the river before realising the man was missing.
His body was found 2km (1.2 miles) downstream on Thursday night, police said. The crocodile was shot and killed.
Local media reported he was from a nearby remote community.