Increasing pressure on shared water resources has often been a driver for the development and utilisation of water resource models (WRMs) to inform planning and management decisions. With an increasing emphasis on regional decision-making among competing actors as opposed to top-down and authoritative directives, the need for integrated knowledge and water diplomacy efforts across federal and international rivers provides a test bed for the ability of WRMs to operate within complex historical, social, environmental, institutional and political contexts. This paper draws on theories of sustainability science to examine the role of WRMs to inform transboundary water resource governance in large river basins. We survey designers and users of WRMs in the Colorado River Basin in North America and the Murray-Darling Basin in southeastern Australia. Water governance in such federal rivers challenges inter-governmental and multi-level coordination and we explore these dynamics through the application of WRMs. The development pathways of WRMs are found to influence their uptake and acceptance as decision support tools. Furthermore, we find evidence that WRMs are used as boundary objects and perform the functions of ‘boundary work’ between scientists, decision-makers and stakeholders in the midst of regional environmental changes.