Hi Graham Simon asked me to reply to this however it can get a bit involved so if you require any more information by all means message me.
GPR uses electro-magnetic waves and will not work in salt water due to its high conductivity. Radar has a good range in air because it is non conductive.
GPR will work to some extent in fresh water due to its low conductivity.
The best way to carry out sub seabed survey is to use a sub-bottom profiler, (shallow seismic) system which generally uses a narrow beam high source level acoustic pulse.
Echo’s are returned from layers or objects of different density much like medical acoustic scanning.
Depth of penetration can be very variable dependent on bottom type (density) but on muddy bottoms you can expect to see several metres down. Frequency of burst is usually around 4Khz and can be simple Carrier Wave(CW) or a chirp.
Chirp allows better Transmit/Receive correlation and thus smaller returns can be detected and hence greater penetration can be resolved.
In water depths over 20 meters attenuation in the water column has significant effects (beam spread and attenuation) and it is best to resort to towing a weighted body with the transducers on it rather than deploying on a pole over the side of the ship.
http://www.theshipwreckproject.com