Officers attached to the Police Transport Command interrupted a number of men spray painting graffiti on a train at Cronulla railway station about 6.40pm on September 26.
The men ran away and police gave chase but could not find them. However, officers found a video camera, still recording, at the scene.
Police allege the footage documented numerous acts of graffiti-based vandalism at various sites in Sydney.
After investigations, officers used a search warrant at Cronulla and Lilli Pilli properties about 7.40am Thursday afternoon.
They seized spray paint cans, fireworks, clothing, electronic recording devices and a small amount of cannabis.
Two teenage males — one, 15, of Cronulla and the other, 16, of Lilli Pilli — were arrested and charged with breaking, entering and stealing transport, malicious damage and graffiti-related offences.
An 18 year old Bundeena man, was charged with breaking, entering and stealing, and trespass offences.
The two youths were refused bail to appear in Parramatta Children’s Court and the man was granted conditional bail to appear in Sutherland Local Court.
Commander of the Police Transport Command, Assistant Commissioner Max Mitchell, said officers would continue to target graffiti-based vandalism over the coming months.