You add water in the object tab. And then change the size and position until it gets where you want. using that trench as an example, they put water and made it big enough to cover the entire trench width and length and positioned it so that it only appeared in the trench. You would put the water a little ways below the the top of the trench so it wouldn't spill over on the rest of the land. it is a little tricky to get it exactly how you want, especially if you want a circular area of water.