Learn Hardcore Japanese: eki no minamigawa ni syoten ga arimasu. - There is a bookstore on the south side of the station.

The genitive の links two nouns to show possession or association. 駅の南側 literally means “the south side of the station.” It indicates that 南側 belongs to, or is a part of, 駅.

Why is に used here? Could we use で or へ instead?

The particle に marks the location where something exists when used with the existence verb あります. You cannot replace に with で, because で marks where an action takes place, not where something simply exists. へ indicates direction or movement, so it’s also not suitable for stating existence.

What does が mark in 書店が? Why not use は?

が marks 書店 as the grammatical subject or new-information focus: “there is a bookstore.” Using は instead (as in 書店は) would make 書店 the topic and imply contrast or prior context, e.g. “As for the bookstore, …” You could also say 駅の南側には書店があります to set 駅の南側 as the topic.

What does あります mean here, and why not います?

あります is the intransitive verb meaning “to exist” or “there is/are” for inanimate objects. You use います only for animate beings (people, animals). Since a bookstore is inanimate, あります is correct.

Why is 書店が placed before あります? Could we reorder the sentence?

Japanese follows a subject-object-verb (SOV) order, but with existence sentences the pattern is fixed as (location) に (subject) が/は (verb). You can move adverbial phrases around, but the verb usually stays at the end. You cannot say 書店があります駅の南側に; however, you can create a relative clause like 駅の南側にある書店 when you want to modify another noun.

What’s the difference between 南 and 南側?

南 simply means “south,” whereas 南側 means “south side” or “southern side.” 駅の南 could mean “to the south of the station” in a general sense, while 駅の南側 specifically refers to the station’s southern side or area.

Can we say 駅南側に書店があります without の?

Dropping の is generally ungrammatical here. You need の to link 駅 and 南側. However, in very casual spoken Japanese you might hear 駅南（えきみなみ） as a fixed place name, but that’s an exception, not a general rule.

When can we omit 書店が and say 駅の南側にあります?

You can drop 書店が if the context already makes clear what you’re talking about, because Japanese often omits subjects to avoid repetition. For example, if someone asks “Where is the bookstore?” you can simply answer “駅の南側にあります。”

How would you say “There isn’t a bookstore on the south side of the station”?

You replace あります with its negative form ありません:
駅の南側に書店がありません。
This means “There is no bookstore on the south side of the station.”