In 2001, the Murray-Darling Basin Commission (MDBC) initiated a program to improve fish passage along 2225km of the River Murray, from the sea to Hume Dam, including the construction of 15 new fishways. The three disciplines of biology, hydraulics and engineering are inherently linked in fishway design. As such, a Fish Passage Taskforce (FPTF) was established to recommend fishway design criteria and comprised a team of scientists, engineers, managers and river operators. In order to complement the FPTF, a team of freshwater fish scientists from three states of the Basin (NSW, Victoria, South Australia) was also created to quantitatively assess fishway performance and any associated longer-term benefits from improved fish passage. The rigour instilled in the design process by the integration of the three disciplines was crucial to the overall success of the program. The FPTF has provided a good model for interdisciplinary cooperation and integration of ideas in relation to the conceptual design, construction and monitoring of fishways, setting objectives according to the characteristics of native fish species. An adaptive management approach to fishway design was taken, thus leading to constant design improvements, optimisation, and improved cost-effectiveness as the construction program progressed. The program had a strategic, holistic view and a strong ecological basis, recognising that fish migration can occur over hundreds, and occasionally thousands, of kilometres.