Word choice, mostly. You choose the words you believe fit the story best. Take this picture, for example (s).
If you were writing a story about a character returning home, it might go like this:
The dank, earthy smell of the bayou settled deep into the back of her throat. She could taste the muggy air, already warm despite the early hour. The Spanish moss hung lazily from the tall branches and the waters were placid, save for where the occasional breathing turtle disturbed it. Irregular patches of sunlight filtered through the branches and illuminated the brackish water.
If you were writing a creepy story about a character who doesn’t like bayous, it might go like this:
There was not an inch of dry ground in sight. What was not murky water of unknown depth was muck or rotting logs ready to give way with the slightest touch. The Spanish moss drooled over the tree branches. She could feel it tickling her neck whenever she passed under it. The sweet, rotting smell of old wood and decaying plants stuck to the back of her throat like phlegm.
In the first piece, I discussed the bayou in positive sensory terms. I talked about the “earthy smell”, which has a positive connotation. Maybe you thought of gardening dirt or petrichor or something similar. I mentioned the warmth, which is good. Everyone likes being warm. Everything is quiet: the Spanish moss isn’t moving (lazily, I might add) and the water is placid - notice I used placid instead of deathly still or dead. There is some life here: I mentioned turtles, which have positive recognition for most people. I could have chosen alligators or snakes or alligator gars, but I chose nice, boring turtles. I mentioned that there is sunlight and it illuminates. People have a subconscious fear of the dark. Put them at ease - at home - with a reminder there is light.
In the second piece, I used some of the same sensory terms worded a different way. For example, the “earthy smell” became “sweet, rotting smell” and your mind takes you back to old sheds, abandoned buildings, dead bodies, and the like. I also mentioned how scents feel in your head in both pieces. In the second one, I said it “sticks like phlegm”. No one likes having mucus build up in your throat. Negative connotation. I played on some primitive fears, like the fear of falling into deep water, the fear of falling period, and that nasty feeling when something weird is touching the back of your neck.
I chose setting to demonstrate atmosphere because it’s easiest to do. You can apply this lesson to character descriptions - enemy soldiers will seem harsher, meaner, uglier, etc. than their friendly counterparts - and emotions - foaming rage instead of irritation - as well. I did a post on atmosphere in horror stories here.