The lower Burdekin is a highly productive irrigation area producing some of the highest yields and highest quality sugarcane in Australia. It is also an area experiencing pressures to expand its irrigation and agricultural activities, and there is concern about the potential long-term impacts of current, changed, and new land and water management practices. These issues are being addressed through the Lower Burdekin Initiative (LBI), which has brought a range of organisations together in an industry/science partnership to address current and future water needs of the lower Burdekin. The initial focus has been on developing a framework to help identify key issues and knowledge gaps, and on better integrating the water related research in moving towards a more coherent understanding of how the whole system functions. In this paper we highlight some of the challenges involved in developing the LBI, including the need for effective collaboration based on good communication and trust, abilities to deal with and communicate about sensitive issues, and improved understanding of the tensions between scientific rigor and industry relevance. To succeed all partners must develop improved capacity and understanding of the issues involved, so that the real pressure points are identified and efforts focussed on the causes rather than the symptoms. There are currently more than twelve activities addressing different aspects of irrigation and water related management within the lower Burdekin and we highlight specific progress with some of these activities.