Trees are very possible, there's a good amount of models for them. As for waterfalls, in the map I'm working on right now, I plan to have at least one, so after I get it to work (I don't know how to make them, but I have an idea) I'll post the results and instructions here (if you haven't already figured it out).
And to access the models in the game:
1. Extract the .md3 files from the 'assets0.pk3' file (it could be assets1, I forgot) which is located in the 'base' folder
2. Put the .md3 files (which are the models) in a new folder in the 'models' folder, located under 'base' as well.
3. Now, in JK2Radiant, right click on the grid and a menu should show up. Select on 'misc' option then select 'misc_model'.
4. A box (known as a brush) will appear on the grid and the 'entity menu' should appear along with a window asking to specify the .md3 file you want opened. So use that window to look in the folder with the .md3 files you created.
5. Choose the .md3 file you want then click 'open'.
6. Here is the tricky part, depending on how you look at it. An error message will pop up, but don't pay attention to it.
7. On the entity menu there are two boxs on the bottom, one that says 'key' and one that says 'value'. In the value box will be written the file path that leads to the .md3 file you opened. It should read something like this:
Now clear all the text before 'models' so it looks like this:
models/****************** (the asterisks being the name of your folder you created and the .md3 file you chose.
8. Now exit the entities menu by pressing the N key and save your map. Exit JK2Radiant and start it back up, and your model should be there.
I know it seems overly complicated but at the moment it's the only way to use models at the moment
You can import a lot of models at a time though, before you have to restart JK2Radiant, you don't have to restart it after every model you put in.
If you have any more questions post them here and I'll try to answer.