Verhaeren, who was technical director with the Dutch Swimming Federation, will replace Leigh Nugent, who resigned in March in the wake of the scandal surrounding the behaviour of some members of Australian team at the London Olympics.
Australia, once a powerhouse in the sport, won just one gold medal in the London pool and Swimming Australia have instituted root and branch reforms this year after a series of scathing reports into team behaviour and management systems.
Gold medals for James Magnussen, Christian Sprenger and Cate Campbell at this year's world championships in Barcelona were an improvement and Verhaeren will be expected to build on that base before the Rio Olympics in 2016.
"To become the best in the world requires four key links in a chain," John Bertrand, president of Swimming Australia, said.
"World class administration of the sport, world class technology, world class athletes - both as individuals and as a team - and world class coaching.
"High performance teams require strong cultural values of trust, integrity, transparency of communication, respect for others and having fun. Jacco lives all of these values.
"To be world best, we must search the world for the very best people and we believe we have done this in appointing Jacco Verhaeren as our new national head coach, to work with our existing world class athletes and coaches."
Verhaeren, who has coached the Dutch swimmers at the last five Olympics and eight world championships, will take up his post in January.
The 44-year-old was in charge when Van den Hoogenband won 100 and 200 metres freestyle gold in the 2000 Sydney Olympics and retained his title in the shorter distance in Athens four years later.
De Bruijn won three individuals golds in Sydney and retained her 50 metres freestyle crown in Athens during a career where she also claimed five world titles.
At London last year, Ranomi Kromowidjojo won the women's 50m and 100m freestyle crowns back for the Netherlands and helped the 4x100m freestyle team to silver in the relay.
"Australian swimming is extremely well respected on the international stage and to have the chance to work with the athletes and coaches in this role is humbling," Verhaeren said.
"In the Netherlands we are a small swimming nation that has worked hard technically to maximise every opportunity. We've had some success working on those technical elements and I hope to bring that focus and drive to this new role in Australia.
"To have the competitive edge in international swimming you have to combine the physical, psychological and technical components of our sport, and I'm looking forward to challenging and inspiring the athletes and the coaches to achieve their goals."
The Dutchman's first task will be to prepare teams for next year's Commonwealth Games in Glasgow, where they will be expected to dominate the pool, and the Pan Pacific championships on the Gold Coast.