Thank you so much for the quick reply! To answer your questions:
1. Great question, and one I always try to ask (along with "do we even need a model here"). Since we're trying to simulate the transport of microplastics in this estuary, we need a 3D model in order to explicitly track the surface velocity of the water, which should provide more accurate results compared to empirical approaches layered on a depth averaged model.
2. Z layers are currently implemented using the sigma layer approach, and there's no thermocline stratification in the model.
3. Should have been more clear here, but PEI is the island at the southern edge of the estuary. In the observations, water levels at this point track those in the rest of the domain; however, in TELEMAC-3D, they're lagged due to a delay in propagating around the island.
I mentioned tidal energy, but I see you mean, and speed makes more sense. The 3D model is producing a delay in propagating the water levels over the shallower areas, which creates the incorrect signature.
Hopefully this clarifies things somewhat- I'll also take a look at a fixed z-layer approach and see if there's anything there