The map of Faerun might make no sense to an earth geologist, but if one would ask a sage in the forgotten realms he could tell you why and how it is how it is...
There are large deserts created by death magic (underground phaerimm activity that destroyed Netheril), Jungles lived in and expanded by Yuan-Ti praying to Zehir, large marshes caused by powerful spells (the kilmaru swamp in Haluraa), rivers flowing out of portals to the plane of water, giant rifts in the land where parts of the underdark collapsed - and of course all kinds of other things caused by actual gods walking the planet.