Determine relative positioning of objects in a confined underwater environment (small tank of water)

Not clear what you are describing - you say the transducer is mounted inside a water meter (I'm envisioning a water flow/totalizer meter like is connected to my house, i.e. something about the size of breadbox or smaller), and then you say a hydrophone (same as transducer?) is mounted on a 3d gantry that moves around the water meter, then you say (3rd sentence) you are mounting the water meter to the frame of the gantry...which I think you mean the gantry is attached to the wall of the water meter?

Maybe a sketch would clear things up?

Bottom line is - if I'm reading your mind correctly - you want to move a hydrophone around inside the case of something bigger, and know where the phone is relative to the bigger case. My answer would be to measure where the gantry moves relative to its mounting points, and then to also know where the gantry mounting points are relative to the case where it gets mounted. Presumably you will send a signal, or count revolutions of a stepper motor or similar actuator that moves the 3d gantry, and would know from those signals and your measurements where the hydrophone is subsequently located. Doing all of the setup work on a lab bench, where you could directly measure and calibrate your gantry control/signal systems might help a lot too.

Are both the hydrophone and the "water meter" mounted on the frame ? ... can't be ??

We're talking small distances, right ? I like the idea of stepper motors to control to the position of both sensors, like two sets of x- and y- axes. Else maybe something like a camera focus ?

"Hoffen wir mal, dass alles gut geht !"
General Paulus, Nov 1942, outside Stalingrad after the launch of Operation Uranus.