applicability of CE-QUAL-W2 for wetland-river system

We plan to study the hydrodynamic (HD) and water quality (WQ) of a river and a wetland and the linked between them. It is necessary to have in mind:

-It is required simulated the HD and WQ in the river
-It is required simulate the HD and WQ in the wetland
-The wetland is located parallel to the river and the linked is through channels. The flow direction depend on the water level in both subsystems (river and wetland)

We have the next concern: The assumption of "The governing equations are laterally and layer averaged" made by the model, let the model be appropriate for the described scope?