eWater was established in July 2005, the result of a merger between two former Cooperative Research Centres – the CRC for Catchment Hydrology and the CRC for Freshwater Ecology. Both CRCs had been operating since the early 1990s and provided eWater with a foundation of well-established science and a team of enthusiastic and experienced people.

eWater retains strong partnerships established by its predecessor CRCs and incorporates a number of new participant organisations with new skill bases, end-user networks, intellectual property and specialist knowledge.

eWater CRC began operations during September 2005, and was officially launched on World Water Day, 22 March 2006.

eWater is governed and managed by eWater Limited (ACN 115 422 903), a company established by the eWater CRC participants, with an independent, skills-based board.

eWater has head office in Canberra; eWater people also work from participant offices located across eastern Australia.

The eWater Participants' Forum, comprising representatives of the CRC's 41 participant organisations, meets regularly to enable the eWater Board and Executive to outline and discuss strategic approaches and operational processes with participant representatives.