Ningaloo was the first place in Australia to allow commercial in-water interactions with humpback whales. DBCA began a trial in mid-2016 with licensed whale shark operators, continued it through 2023, and transitioned it to a licensed industry from 2024. Swimming with humpbacks is only permitted in Ningaloo Marine Park (State waters) and the Muiron Islands Marine Management Area, and operators carry electronic monitoring so their interactions are tracked in real time.

Each winter roughly 40,000 humpback whales migrate along the WA coast, passing Ningaloo northbound to calve in the Kimberley and southbound with calves in spring; they can often be heard underwater during dives in Lighthouse Bay and the Muirons. On a swim tour, spotter aircraft and crew identify whales whose behaviour suits an interaction, and small groups are placed in the water ahead of them. Encounters range from a whale passing below to curious animals approaching closely. The program's principles include minimising impacts on mothers and calves and managing swimmer safety.

Outside licensed tours, general law prohibits swimming within 100 m of a whale, and anyone approached must try to keep 100 m away. The experience is a snorkel in open ocean and suits confident swimmers. Many operators combine humpback swims with manta rays, reef snorkels and, early in the season, late whale sharks. Water in the humpback season is cooler than in whale shark season, so a thicker wetsuit is worthwhile, and the same trip frequently produces manta rays and dolphins. Humpbacks can also be seen breaching from Lighthouse Bay and the Muiron boats, and heard underwater on most winter dives around the Cape.

Book a licensed humpback swim tour in Exmouth or Coral Bay. Exmouth tours depart Tantabiddi boat ramp (35 km from town, operator transfer included); Coral Bay tours leave from the Coral Bay boat ramp. Spotter aircraft and crew locate suitable whales outside the reef; small groups are placed in the water ahead of the whale's path.

Tours run most of the day (typically 7–8 hours) and include lunch, wetsuits and snorkel gear; book well ahead for August–September.

Open-ocean activity outside the reef: cancelled in strong south-westerly winds or large swell, which are common in winter. Water is cooler (21–24 °C) than whale shark season. Swimmers must cope with swell and deep water.

Morning departures avoid the afternoon sea breeze. Tours are cancelled if the swell or wind makes in-water interactions unsafe, and operators may reschedule to the next suitable day.

Snorkel only. Enter quietly when directed, stay with the guide and the group, and let the whale choose how close to come; do not chase or approach. Return to the boat promptly when called.

Snorkel only.

DBCA-licensed humpback interaction operators (the trial began in 2016 among licensed whale shark operators and moved to a licensed industry from 2024), including Exmouth and Coral Bay whale shark operators such as Exmouth Dive & Whalesharks Ningaloo, Ningaloo Whaleshark Swim, Kings Ningaloo Reef Tours and Coral Bay Eco Tours.