Swimmers at a Darwin public pool got a fright this morning when a baby crocodile was spotted in the shallow end.

The 40cm freshwater crocodile was scooped up by a lifeguard at the pool in Parap, an inner northern suburb.

Lifeguard Tim Dupe says, not long after he opened the pool, a swimmer told him there was a croc in the shallow end.

"I thought he was joking, I thought it must have been a rubber one," he said.

"I said, 'nah, is it a real one?' and he said, 'yeah'.

"I went down the shallow end and in lane six, right up in the corner, was a little freshwater croc, so I grabbed the leaf scoop and scooped it up."

Mr Dupe says it was probably a prank.

"I think it has been put in here by somebody," he said.

"It is pretty dry all around the place, so it is not as if there have been any crocs living in here.

"Someone must have jumped the fence or got in here and thrown the croc in the pool."

The croc was taken away by Parks and Wildlife Rangers.