Yes, there are alot of factors in play to detect a corpse scent underwater.
Research shows value of cadaver dogs locating underwater corpses
"When a body is on land it is hoped it will stay in one place, but in water a body can move in three dimensions, so it is a lot more difficult to locate and recover"
.. research has found that the dogs can only be really effective if they can get down to the level water to clarify the scent or they may not be able to give a clear indication.
Therefore, access to the water both from the bank and particularly from a boat is crucial to the success of a search. "If the sides of the boat are too high, the dog will simply not be able to smell the water".