In Surveyor 2.0 open the Layers Palette (if it is not already shown on the screen open the Windows Menu and click the name Layers Palette to put a tick next to its name).
Any Water Effect layers will appear as listed in the Layers Palette under the Effect Layers section. If you have several effect layers present and you are not sure which one it is just toggle off/on the "Eye" icons next to each layer name to hide and show it. When the water vanishes you have identified the correct layer. To delete it just right click on the layer name and select Delete.
PS: The most common reason for this issue (but not necessarily true in every case) is when you import into TRS22 or Trainz Plus an older route that has legacy water features. TRS22/Trainz Plus will convert the legacy water to a Water Effect Layer with "Legacy" in its name. The two water features, Legacy Water and Water Effect Layers, do not "play well together".