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?

KeepItSimpleStupid

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.