السماء فوق المدينة.

In Arabic, the present-tense verb to be is usually not stated.

So السماء فوق المدينة is a normal present-tense nominal sentence:

• السماء = the topic, the sky
• فوق المدينة = the comment/predicate, above the city

Arabic expresses the idea directly, and English adds is when translating.

If you wanted was or will be, Arabic would normally use a verb such as كان.

A careful MSA pronunciation with full case endings is:

as-samāʾu fawqa al-madīnati

A more pause-style reading, which is very common, is closer to:

as-samāʾ fawqa al-madīna

A few useful notes:

• السماء ends in a hamza, so the end is a glottal stop: -māʾ
• فوق is pronounced fawq
• المدينة is al-madīna

Because س in السماء is a sun letter, while م in المدينة is a moon letter.

So:

• السماء is pronounced as-samāʾ, not al-samāʾ
• المدينة keeps the l sound: al-madīna

The spelling stays the same, but the pronunciation changes with sun letters.

فوق means above or over.

In grammar terms, it is a word of place, often treated like an adverbial expression of location. In simple learner terms, you can think of it as a word that tells you where something is.

So:

• فوق المدينة = above the city

Because فوق needs something after it to say above what.

So:

• فوق = above
• المدينة = the city

Together, فوق المدينة means above the city.

Arabic places the location expression after the noun being described here:

• السماء
  • فوق المدينة
• the sky
  • above the city

With full case endings, it is:

السَّماءُ فوقَ المدينةِ

More specifically:

• السَّماءُ ends with -u because it is the subject/topic of the nominal sentence
• فوقَ ends with -a
• المدينةِ ends with -i because it comes after فوق in this construction

In normal Arabic writing, these short vowel endings are usually not written, which is why you see السماء فوق المدينة.

Because both nouns are definite:

• السماء = the sky
• المدينة = the city

Arabic uses ال to mark definiteness, much like English the.

Without ال, the sentence would become much less specific:

• سماء فوق مدينة would mean something like a sky above a city, which is not the natural idea here.

Not exactly.

• فوق usually emphasizes above / higher than
• على often means on / on top of / upon

So if there is no idea of physical contact, فوق is often the better choice.

Examples:

• الطائرة فوق المدينة = the plane is above the city
• الكتاب على الطاولة = the book is on the table

السماء is feminine in Arabic.

You do not see that clearly in this sentence, because there is no adjective or verb showing agreement. But if you added an adjective, it would be feminine:

• السماء صافية = the sky is clear

Here صافية is feminine to match السماء.

Yes, Arabic word order is somewhat flexible, but the sentence as given is the most straightforward and neutral:

السماء فوق المدينة

You can sometimes move the location phrase forward for emphasis:

• فوقَ المدينةِ السماءُ

That is less neutral and more marked stylistically. For a learner, the original order is the best one to use first.