Place your water entities on the map where your lake/sea and/or river are going to be. Then use the height tool to make the ground under the water entities lower.
Then go to heights and set water altitude as anything below zero, like perhaps -10. You will now see all your water entities being lowered to -10. Continue to lower them by using the water altitude settings until it looks ok.
I have added a screenshot of a map that I am working on (very very WIP) and I´ve encircled the part of the menu where you set the water altitude. I hope this will explain how to set the water altitude. By doing this, all soldiers and vehicles that enters the water, will have splash around them when moving and if the water gets too deep for them, soldiers will swim and vehicles will sink and be lost forever.
~Zeke.