Ecohydrological modelling and prescribing environmental flows (e-flows) is significant in the Integrated Water Resources Management (IWRM) practice. However, for many river basins, there is lack of data on ecosystems and on the relationships between e-flows and ecosystem functioning. This lack of sufficient ecosystem data is mostly addressed in ecohydrological modelling by using hydrological metrics as surrogates of river ecosystem. In this study, we are demonstrating how it helps e-flows modelling and real-life management decisions underway with respect to Inter-basin Water Transfer (IBWT) projects. Desktop model ‘Flow Health’ is used here to design e-flows regime for Chalakkudi Sub-basin in Southern Peninsular India. Chalakkudi Sub-basin is over abstracted with six large dams built as components of the Parambikulam Aliyar Project (PAP), Asia's largest IBWT network. The monthly e-flow regimes required to maintain alternate levels of ecosystem conservation are estimated in this paper. The additional flood flow volume required for these alternate levels is also discussed. The results are useful in the stakeholder engagement process for informed decision-making on e-flows and redefining the IBWT operations within a broad framework of IWRM.