A man faced court on Monday charged with allegedly shooting at a jet-ski rider from a houseboat on the Murray River.

Police were called to the Murray River near Moama about 4pm on Sunday where they were told at least two shots were fired at a 23-year-old man, who was riding a jet-ski. Witnesses told police the shots appeared to have come from a nearby houseboat.

Police searched a houseboat and a home on Goldsborough Road, Moama where they seized ammunition, cannabis and three firearms, including a shotgun found under a lounge chair on the houseboat.

A 51-year-old man, who holds a firearms licence in Victoria, was arrested and charged with firearms offences.

He was formally refused bail at Wagga Wagga Local Court on Monday.

Inquiries are continuing.