Hi,

Following are some of the best universities in India that offer M.Sc in applied Geology:

1. IITs - Roorkee,Kgp,Bombay

2. UNIVERSITY OF DELHI

3. BANGALORE UNIVERSITY

4. ALIGARGH MUSLIM UNIVERSITY

5. UNIVERSITY OF CALCUTTA

6. PONDICHERRY UNIVERSITY

7. BANARAS HINDU UNIVERSITY

Now out of these you may try in bangalore university, aligarh muslim university or university of calcutta as the admission process are already going on in other universities. Else, you can go for private institutes. The admission procedure is likely to be availble for many private universities. So, you can contact the specific college's authorities regarding the same. 

Hope this helps, good luck!