If you unfortunately hit a ball into a water hazard you can edit that shot in the editing process on the user interface. You do this by selecting the shot that went into the hazard, then left click on the "Water" icon. Shown below.
Once the shot has been marked as finishing in a water hazard, a "X" node will appear. You can then move the "X" node to the water hazard where the ball ended up. A penalty shot will automatically be added to the hole.