Water shortages are forecast to affect 50% of the world's population by 2030, impacting developing nations most acutely. To increase water security there has been a significant increase in Inter-basin Water Transfer (IBWT) schemes, engineering mega-projects that redistribute water from one basin to another. However, the implementation of these schemes is often contested, and evaluation of their complex impacts inadequate, or hidden from full public scrutiny. There is an urgent need to develop more integrated, holistic, and transparent ways of evaluating the multiple interlinking impacts of IBWT schemes of this scale. In this paper, we address this gap by outlining an experimental methodology to evaluate IBWT schemes using a multidisciplinary and transparent methodology which utilises publicly available data. We illustrate the method using a case study from the Inter-Linking Rivers Project in Northern India, comparing the results of the experimental approach against the official analysis of the proposed scheme produced by the State Government of Jharkhand. The results demonstrate that the proposed experimental method allows more detailed evaluation of spatial and temporal variability in water availability and demand, as well as holistic evaluation of the functioning of the proposed scheme under different future scenarios. Based on these results we propose a flexible framework for future evaluation of proposed water transfer schemes which embeds the principles of integrated assessment, transparency, and sound science which can be adapted to other IBWT projects across the world.