Dear Vaibhav

Depends on how far along you are in the process of becoming a civil engineer.

• If you are still pursuing your degree, then you can apply to the jobs through UES. It is for Navy and Army. It involves the process of a college level interview and national level interview. This is great for someone who wants to go into defence but the only disadvantage being that it is a short service ranging from 10 to 14 years.Next if you are already done with your degree, then you can try for IES exam conducted by UPSC every year in June. This is comparatively better and you can get into MES which is military engineering services but its entry is a bit tough so you will need to prepare for it.
• If you are interested in research for defence then you can try for DRDO which deals with R & D.
• You can always keep following the websites of the defence organizations for jobs in Naval architecture, design, coastal engineering, ground control work, etc.

It all depends on what you wanna pursue in defence. 

• If you have masters, there will be jobs related to your specialization as well, just Google it and check the websites. Even UPSC keeps posting these jobs. 

Good luck