Waves forces on a structure are often calculated by Morisons Equation. This states that the total force on an object is the sum of the drag forces and the inertia forces.
The drag is a result of flow past the member and depends on the shape of the member (form) and friction (skin friction) and dependent on viscous effects of the fluid.
The inertia is a result of the fluid particles resistance to being accelerated or decelerated. For any object to be moved work needs to be done on the object. However, for a submerged object work not only needs to be done on the object, but also on the surrounding medium to move it out of the way. Hence the total work required is greater than that soley required to move the object. It is the same as 'adding mass' to the object to take account of the fact you need to move the water as well as the object.
To give an example of what Ussuri said, when calculating ship berthing energies to platforms or docks, there is a mass of water that is moving with the ship. If you stop the ship, this water continues its motion and produces an additional inertial force.
