One of the most effective ways to create a memorable natural fantasy location is to base the environment upon the contrast between two typically opposite natural elements, such as air and earth or ice and fire.
Common examples include icy plains dotted with bubbling geysers and rocky deserts swept by the wind, but you could also have oceanic depths inhabited by electric creatures.
In a similar vein, the contrast between old and new, artificial construction and natural regrowth, adds personality to a location and often provides clues about who lived here in the past and how things have changed over time. The result should be a form of dynamic balance, and can also elicit feelings of melancholy or wonder in the travelers.
For instance, a vast horizon of skeletal skyscrapers overgrown by vegetation and taken over by the nests of gigantic feathery creatures; or an endless grassland where herds of bovine calmly graze in the shadow of rusty, titanic war machines.
The goal of such a location isn’t purely visual – it represents a fragile environment that is worth protecting and a precarious peace that has been achieved, certainly not without pain, over the course of the centuries.
Partially continuing from the points above one of the best ways to make a location look alive is to populate it with creatures whose appearance, behavior, and abilities are strictly tied to their environment.