A good Samaritan who rescued a man in trouble in the harbour at Balmain in Sydney's inner west says he is not deterred from offering future help to strangers, despite allegedly being assaulted and left to swim to shore.

The rescuer assisted a 23-year-old man by letting him on board his small boat, only to then end up fleeing the boat himself.

Boat owner David Hannon said he jumped into the water fearing for his safety after the man became "aggressive".

The 23-year-old then allegedly headed further offshore in the boat, and Mr Hannon was left to return to shore with the help of emergency services.

Police with the assistance of Marine Area Command and PolAir found the man in the vessel a short distance away, and he was then arrested and taken to Royal Prince Alfred Hospital for assessment.

Acting Superintendent Sam Crisafulli said the man was "most likely" under the influence of drugs and has now been charged with assault and unauthorised use of a vessel.

The 24-year-old was "very aggressive", according to the rescuer. ( ABC News )

Mr Hannon said it was a more eventful night than he would have liked.

"I decided I was going to take my chances with the bull sharks," he said.

"So I dived into the water, he took off in the world's slowest get away boat, it's an 80-year-old putt-putt."

Mr Hannon said he would be blaming his wife for the strange encounter.

"They always send you downstairs to investigate the noise, always with the caveat, 'Be careful'," he said.

But he said he would not be deterred from helping strangers in the future.

"If someone calls for help on the water, you go and help them," he said.

Time to buy some binoculars?

While the incident unfolded, a man in a nearby unit block on Wulumay Close in Rozelle was holding a rifle at the PolAir helicopter.

However, it is believed the 47-year-old was actually using the rifle's telescope to get a better look at what was happening on the harbour.

Acting Superintendent Sam Crisafulli said it was a "foolish decision" despite the fact that the firearm was not loaded.

"Other residents could see what he was doing … police received a number of phone calls from residents."

He has now been charged with not keeping the firearm safe, not keeping ammunition stored in a locked container, unauthorised use and handling a firearm under the influence of alcohol.

He was granted conditional bail.