Mountains stop air pollution spreading.
in SC4 Water pumps need to be close to non-polluted water source. (no matter regarding if it's a river or a lake). Only water tour can be build far from water but their efficiency is very low in comparison with waterpumps
Also if you don't create river connected to the edge of the city the commercial port won't be in use since it only works by exchanging hypothetic goods with to other cities.
But the main natural elements which affect gameplay is Tree (Not sure if there is difference between trees you grow yourself and the one from area editor mode). They can do miracle. Trees can:
- stop and absorb pollution
- improve need for High Tech Industries nearby
- raise quality of life of sims.
- can also stimulate the need for high density residential area and then make close building grow
I love them, they really are the best tool to enhance a well build city (remember that you can plant trees on existing building free space (garden, park, road side, etc...)