Yes, you can do Mtech in Environmental Engineering either if you do Bio-technology in Btech, there is no any restrictions of doing it. If you got a seat in environmental stream in counselling then you can do specialization in it. 

Hello aspirant,

Yes, you can pursue your masters in Environmental engineering after completion of your B.tech in Biotechnology even though it is one of the specilizations in Civil engineering.One of the ways to do M.tech in environmental engineering is through GATE where you can join in IITs, NITs offering this specilization.

I hope this is helpful to you.

Hey lareb,
According to your query,
Yes definitely!!
You can opt for environmental engineering mtech after completing btech in biotechnology.  I would prefer you to take admission in reputed govt.  Or private colleges to complete your mtech for getting good academics and better initial placements.
Hope you find it useful.
Thank you.