Water Institute is an interdisciplinary Research Centre established in 2008, which facilitates innovative research, education and training. Several faculty members of Karunya are carrying out interdisciplinary research on water in this Institute.  The Institute aims at  on achieving scientific water management and water security for all, especially those in the semi-arid zone.

The Mission of Water Institute is to impart higher education, to carry out research, to build capacity and to solve location specific problems for achieving sustainable water management, especially in the semi-arid zones.