The Marine Science and Diving program at St Mary's is one of the best and longest running school marine science programs in Australia.

St Mary's was the first school internationally to take part in a Mingan Island Crustacean Study (MICS) research project, identifying whales off Canada, and the first school from Australia to participate in the Aquanaut program in Florida, in which participants spend days and nights living under water.

St Mary's is one of a handful of Australian schools to offer the Master Diving program within the school curriculum.

From time to time there are also opportunities for students, who undertake these subjects, to be involved with Marine Science and Diving tours in Western Australia (Albany, Exmouth and the Abrohlos Islands) and overseas (the east coast of the US and Canada, and Mauritius).

Students can opt to study Marine Science in Years 9 and 10, and Years 11 and 12 ATAR courses. The course aims to foster an interest in the marine environment, physics and biology and an environmental awareness through the marine setting. It is also designed to provide students with an opportunity to conduct a true scientific research project. Students study Oceanography, Snorkel Diving, Maritime Archaeology focusing on the wreck of the Batavia, Marine Biology of Cetacea and the Physical Oceanography of the beach.

Students are introduced to long-term research in Year 9 where they raise and conduct investigations on a yabby, and then conduct their own research in Year 10, ranging from Marine Biology, Scientific Diving, Marine Engineering, and Underwater Robotics. The research topic is chosen by the student and worked on through the year. Visits are made to the Marmion Marine Park, AQWA and the Bunbury Dolphin Discovery Centre.