The Aquatic Zoology department is responsible for documenting and researching most of the marine, estuarine and freshwater faunal groups of Western Australia, and in some groups a terrestrial component as well. Similar fauna in related regions are also studied for comparison.

Aquatic Zoology surveys and studies varying climatic regions, from the cool temperate waters of Western Australia's south coast, through to the warm tropical waters of the northwest atolls, and even the deepwater areas off the WA coast. Additionally, freshwater and some terrestrial fauna (such as land snails) are studied.

The department's staff have strong taxonomic research backgrounds, and the department produces scientific papers, reports and popular books on a regular basis.

Aquatic Zoology's staff have considerable experience in marine fieldwork and expertise in a wide range of phyla. The department frequently collaborates with scientific colleagues at other museums, universities and government departments. Consequently, they undertake fieldwork that produces large data sets giving excellent overviews of species’ distribution and populations. This is especially important for assessing the biodiversity of an area and for detecting any changes that might have occurred. This knowledge is vital for the management and protection of marine habitats. Voucher specimens from such work are lodged at the Western Australian Museum for future reference.

Specimens from deeper water trawling and dredge sampling surveys also form an important part of the department's research. In recent years, such work has been carried out in collaboration with the Australian Institute of Marine Science (AIMS), the Commonwealth Scientific and Industrial Research Organisation (CSIRO) and the University of Western Australia (UWA).

The Aquatic Zoology department plays an important role in the development of both temporary and long-term museum displays. Offsite displays are also prepared for events such as for Seaweek, or for other organisations such as Scitech and the WA Fisheries Naturaliste Marine Discovery Centre, and for industry exhibition spaces such as the Woodside North West Shelf Visitor Centre on the Burrup Peninsula.

Aquatic Zoology have extensive collections of 'wet' (mainly alcohol-preserved) and dry specimens which are maintained at the Museum's Welshpool site, with the larger specimens stored at a nearby commercial warehouse. There is also a comprehensive image collection of both live and collected specimens.

Specimens are regularly loaned to other scientific experts for research, both within Australia and overseas.