Will it be worth doing mtech in transportation from iit bhubaneswar instead choosing water resources from iit kgp ?

This totally depends upon your interest in the subject. You should give preference to the subject rather than a degree from college because your subject will shape your future.

The school of water resources is one of the pioneer centers for education and training in water quality and quantity management. There is an advanced research water quality lab in IIT Kharagpur. It is an old IIT and will provide more opportunities for higher studies in foreign universities, people also go to foreign universities from IIT Bhubaneswar but opportunities in IIT KGP will be more.

The water resources have limited scope considering the Indian employment scenario. If you are giving preference to the subject then join IIT Bhubaneswar. If your preference is not the subject then join IIT KGP because exposure and opportunities will be more in IIT KGP. A student planning for Ph.D. after M-tech will have much better scopes in IIT KGP than IIT Bhubaneswar.