Protest organizer Rising Tide said hundreds of activists were in the harbor near the Port of Newcastle, as part of a 50-hour blockade that started on Friday, Reuters reported.
New South Wales state police said in a statement that two men and a woman were arrested after being removed from the water at the Port of Newcastle on Saturday afternoon.
Rising Tide said in a statement police made arrests after protesters paddled on kayaks past police lines.
Climate change is a divisive issue in Australia, the world's second-biggest exporter of thermal coal and the largest exporter of coking coal.
Newcastle, some 170 km (105 miles) north of Sydney, is the largest bulk shipping port on Australia's east coast and the country's largest terminal for coal exports.
A Port of Newcastle spokesperson said there was no impact to vessel movements due to the protest. A similar protest in November last year disrupted port operations.