For the first time in the Northern Territory's water management history it is facing the challenge of managing an over-allocated groundwater resource. Rapid rural residential and agricultural development in the Howard River catchment of Darwin's hinterland has increased competition for groundwater from the bore-field that supplements the capital's metropolitan water supply. This has generated tensions between different water users and precipitated a water allocation plan for the Howard East aquifer. Initial context analysis indicated a widespread lack of public understanding of groundwater systems and processes, leading to misconceptions about the origin of local groundwater resources, groundwater-surface water interactions, extraction rates and impacts. In addition there is a legacy of mistrust by some peri-urban community members of government-driven planning processes to manage groundwater resources. The main objective of this study was therefore to trial two planning tools suited to this context over a 15 month period: (i) an extended stakeholder analysis and (ii) the participatory development of a 3D visualisation model, via a process described as the participatory Groundwater Visualisation Tool (GVT). The tools assisted the water planning agency to better understand stakeholder needs and interests, contributed to popular scientific understandings of hydro-geological conditions and processes, as well as captured local knowledge and values in preparation for an open and effective planning process.