It is the endpoint of the main shipping channel across Moreton Bay which extends 90 kilometres (56 mi) north to Mooloolaba and is dredged to maintain a depth of 14 metres (46 ft) at the lowest tide.

According to the former Queensland Department of Primary Industries the Port of Brisbane was the most likely entry point of the South American fire ant to Australia.

[8] Deposits of silt and sediment in the ports channels and berths have caused delays of up to five days in the delivery of cargo including oil supplies.

However, due to the height restrictions of the Gateway Bridge and length restriction of 270 metres (890 ft) that far upstream, the larger ocean-going cruise liners must dock further down the river at the more industrial Multi User Terminal at the Port of Brisbane.

[12] The port accommodates a visitors centre and in 2005 a shorebird roost was constructed.

The bird roost is the largest site built specifically for migratory shorebirds on the east coast of Australia.