The sidelobe interference will typically result in a bias towards whatever the interfering boundary velocity is. For the bottom this is a bias towards zero (unless there's a moving bottom) and at the surface it will depend on the sea state or surface wind conditions. The interference is not noise. The sidelobes from the acoustic beam encounter the boundary before the main lobe. Because the boundary is a strong reflector and these sidelobe echoes occur in the range (specifically at the time) where the main lobe range cell is located, they dominate the returned signal in these range cells. For more comprensive understanding of sidelobe interference; consult the Principles of Operation manual.
Unfortunately, there isn't a way in post-processing to separate out the bias effect from the side lobes. You can try to correct the data, but you have to assume some model for the velocity profile, so this isn't necessarily any better than discarding the data and using a model to fill in the gap in the first place.