Brisbane River is still too dangerous for recreational users, two weeks after the city flooded, with large amounts of debris still being located and retrieved above and below the surface.

Kell Dillon, general manager of Martime Safety Queensland (MSQ), said workers are pulling out pontoons, jetskis, yachts and trees from the water, among other debris.

"We're up to about 1,100 tonnes of material cleared off the river surface, but we're finding a lot on the bottom. We've had 160 unknown objects from Hamilton Reach down towards the Port," he said.

"A lot of stuff is still to come out of the river yet. Some is harder than others. … Getting it all off the bottom is quite a task."

Port blocked to larger vessels

Treasurer Cameron Dick said the Port of Brisbane, Queensland's biggest port, which facilitates $50 billion worth of trade each year, is not yet operating at full capacity because debris is preventing larger ships from entering the port. 

"Some of the larger container vessels, 300 metres or greater in length, still can't access the port," Mr Dick said.

"We usually have about 20 ship movements per day, we're already back to 17 per day and the port is operating 24 hours a day."

Sixty navigational aids — buoys and beacons — were also damaged in the floods and are currently being repaired and replaced, he added.

Diving and hydrographic survey teams from the Royal Australian Navy have joined clean-up crews from MSQ and the Port of Brisbane, targeting debris that poses the biggest risk to ships and smaller watercraft.

Speaking from HMAS Moreton on the Brisbane River, Lieutenant Commander Michael Kerrisk said HMAS Shepparton, usually based in Cairns, was surveying water from the river to Moreton Island, while and HMAS Yarra was operating from Moreton Bay to the Caloundra fairway.

"We also have a deployable geospacial team here and they are surveying the river from St Lucia through to Hamilton at the request of the Port, and following those operations, the divers from Australian Clearance Diving Team are working on the final pieces of what is and what isn't an obstruction and hazard to getting the river open again," he said.

"They've been given a list of 49 different dive tasks … and that's looking at the status of the pylons of all the ferry terminals and bridge structures and other hazards, along with the quite damaged and no longer upright markers that keep shipping safe through the Port of Brisbane."

Major General David Thomae said a US Navy supply ship would join ADF crews in the coming day.

"The US Navy has very graciously offered up to 100 people from that ship to support us," he said.

"We'll incorporate them into our normal operations across Brisbane, so you'll see them out on the streets as you see the rest of the Australian Defence Force."

Warning for recreational boat users 

While some restrictions have eased for boat owners to adjust moorings, recreational users are being told to stay off the water.

"It's just too dangerous for recreational purposes," said Mr Dillon, from MSQ.

"What we don't need is disaster tourism — people taking selfies with damaged equipment in the background

"There is still a lot of debris … the currents are still high, the water is very, very dirty and people being on the water obstructs our contractors and staff getting about their jobs and being able to clear the river."

On land, Brisbane Lord Mayor Adrian Schrinner said debris had been cleared from 1,100 streets around the city.

"Our number one priority was to get that stuff off the kerbside as quickly as possible, because people were coming out of their homes and businesses that were looking at these piles and that was their life in front of them," he said.

"We could not have done that without the support of the ADF."

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