You can use Aqua-Sim, NS-2, and Qual-Net for simulation. However preferred will be Aqua-Sim.

http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5422081&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5412664%2F5422059%2F05422081.pdf%3Farnumber%3D5422081

You can use Qual-Net or NS-2 or 3, already many researchers working on these simulations especially for underwater sensor networks. 

Thanks alot guys...... I have no experience in ns-2. keeping this in mind how do u rate the difficulty level in learning Aquasim on a scale 1 to 10.

Moreover does qualnet implement underwater channel, routing and link layer protocols specific to underwater sensor networks. i went through a qualnet tutorial on youtube. what i understood is that qualnet doesn't implement any of those. 

In the case of range based localization you need an emulator as TOSSIM (Tinyos), contiki and coja etc. in order to load the application in real nodes. And in the case of free range localization you can use any simulator (Castalia, Tossim, Matlab etc.)

Dear Sir,

Qual net is the best tool for you. NS2/NS3 having more number of unix commands. For computation work you have to use matalb/scilab