The commercial whale watching industry has experienced a rapid expansion in Australia in recent years, often outpacing regulatory development. While whale watching has the potential to provide a number of benefits to the community, industry and animals, these benefits come at the risk of over-exploiting the animals and their environment. A management regime can be used to regulate the industry through legislation, a permitting system with associated conditions or voluntary guidelines. Such management relies on a well-developed understanding of the animals, the industry and potential and real impacts so that any regulatory measures are effective. There is a need for sound scientific research incorporating short-term tests and long-term monitoring of the whale watching industry, participants and target species to inform and support management decisions. Research should focus on the behavioural ecology and population biology of the animals, the extent of the industry and the expectations and satisfaction of the participants. This information can then be used to develop a long-term management system that will detect trends and impacts and will be responsive to necessary changes.