לא נשאר שום קפה במשרד, אז אני שותה רק מים.

לא נשאר literally means didn’t remain / wasn’t left, so the sentence gives the idea that there used to be coffee, but now it has run out.

• לא נשאר שום קפה במשרד = There’s no coffee left in the office
• אין קפה במשרד = There is no coffee in the office

So אין קפה is more neutral and just states absence, while לא נשאר קפה emphasizes that the coffee is gone.

Here שום means any or no ... at all, depending on the negative sentence around it.

So:

• לא נשאר שום קפה = There isn’t any coffee left / No coffee is left at all

It adds emphasis, a bit like saying:

• not any coffee
• no coffee whatsoever

This is a very common pattern in Hebrew:
לא + verb + שום + noun

Yes, it does. Hebrew שום can mean either:

• garlic
• any / no ... at all

The meaning comes from context.

For example:

• אני אוהב שום = I like garlic
• לא ראיתי שום דבר = I didn’t see anything
• לא נשאר שום קפה = There’s no coffee left

So in your sentence, it definitely does not mean garlic.

Because קפה here is a mass noun, like water, milk, or sugar in English. Hebrew normally keeps it singular in this kind of sentence.

So:

• שום קפה = no coffee / any coffee

You would not normally make קפה plural here.

The verb agrees with קפה, which is a masculine singular noun.

So:

• קפה = masculine singular
• therefore נשאר = masculine singular past tense

Compare:

• לא נשאר קפה = No coffee was left
• לא נשארה עוגה = No cake was left
  because עוגה is feminine singular

במשרד means in the office or in an office, depending on context.

It is made from:

• ב־ = in
• משרד = office

A useful thing to know: in unpointed Hebrew writing, במשרד can represent either:

• be-misrad = in an office
• ba-misrad = in the office

The spelling is the same without vowel marks, so context tells you which one is meant. In this sentence, in the office is the natural meaning.

Because the speaker is describing a current result of the situation.

• לא נשאר שום קפה במשרד = there’s no coffee left
• אז אני שותה רק מים = so I’m drinking only water / so I drink only water

Hebrew present tense often covers both:

• I drink
• I am drinking

So אני שותה can mean either, depending on context. Here it most naturally means the speaker’s present action or current habit in this situation.

אז here means so.

It connects the two parts of the sentence:

• There’s no coffee left in the office, so I’m only drinking water.

In other contexts, אז can also mean then, but here so is the correct meaning.

רק means only, and here it modifies מים.

• אני שותה רק מים = I drink only water

Placing רק right before the thing being limited is very common in Hebrew.

Compare:

• אני רק שותה מים = I’m only drinking water
  (emphasis on the action)
• אני שותה רק מים = I’m drinking only water
  (emphasis on water as the only thing)

So the word order affects what is being emphasized.

Because מים is one of those Hebrew nouns that normally appears only in a plural form, even though in English the meaning is a mass noun: water.

So:

• מים = water

You just learn it as the standard word. It often behaves like a plural grammatically in other contexts, for example:

• מים קרים = cold water
  literally cold waters

But in meaning, it is simply the normal everyday word for water.

Word-for-word, parts of it do line up that way, but that translation sounds unnatural in English.

A more natural English rendering is:

• There’s no coffee left in the office, so I’m only drinking water.

That is a good example of how Hebrew and English often express the same idea differently:

• Hebrew: לא נשאר שום קפה
• natural English: There’s no coffee left

So it’s better to learn the Hebrew phrase as a whole idea, not just as a literal word-by-word substitution.