On the menubar, go to World>Interior... Select the cell you want to have water from the drop down, and then check the box next to "Has Water". Water height is self explanatory from there.
On the menubar, go to World>Regions... Choose new and make a name for the region. Then edit the weather chances. Note: They are based on a percent. If it says 10 in the box next to "Rainy", it means there will be a ten percent chance of rain in that region. This also means that all of them put together must add up to 100.