Hi @matttob,
It’s a bit confusing but the vehicle actually uses VFR_HUD.alt as its pressure-based depth indication (just as a negative value). As far as I’m aware contributions to the vertical position from the DVL should be ignored by EK3_SRC1_POSZ being set to Baro (1), so I’m not sure why your UGPS system is acting unexpectedly.
I’ve asked internally whether there’s some kind of known explanation for what you’re seeing.
As a side note, using the Water Linked UGPS and DVL together is (as far as I’m aware) not yet actively supported, so it’s possible there are some issues with trying to do so.