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We must to survey an area 1 km x 300 m (bathy, scan side, sub bottom) water
depth 50 m, vessel speed 1knot.
It is possible that this small area to be intersected by an old buried
metallic pipe 6 inch diameter (buried maximum 0.5-2 m in sand or mud).
Scan side, sea bed classification and sub bottom can cheat us for such a
small diameter of pipe.
Survey is too small for large investments in magneto. If we can have a tool
to indicate us where to insist with sub bottom profiling job is safer for us.
Do you have suggestions for easy confirm/infirm existence of that kind of
pipe?

[KISS]

Check into ground penetrating radar. Don't know if they are available to work underwater.

[Sitkadiver]

50 meters is too deep for divers using a hand held metal detector to do a very good sweep. I think a towed magnetometer is the best thing for you. Not sure how much is too much of an investment for you, but you can always look into leasing or renting from a commercial dive operater.

If the bottom sediment is thick, there's a good chance a side scan won't see through it, and only show you the bottom.