Pasta na zuby není na stole, je v koupelně.

Yes. Pasta na zuby literally means paste for teeth, and it is a normal way to say toothpaste.

A few useful notes:

• pasta = paste
• na zuby = for teeth / used on teeth

In everyday Czech, you will also often hear zubní pasta, which is another common way to say toothpaste. Both are understandable.

• pasta na zuby = more descriptive, literally paste for teeth
• zubní pasta = dental/tooth paste

So this sentence is natural, even if zubní pasta may be a bit more common in some contexts.

Because na zuby is a fixed, very common Czech pattern meaning for X or meant for X.

Here, na takes the accusative case:

• zub = tooth
• zuby = teeth / teeth (accusative plural here)

So:

• pasta na zuby = toothpaste
• literally: paste for teeth

This is similar to other Czech expressions:

• krém na ruce = hand cream
• lék na bolest = medicine for pain
• brýle na čtení = glasses for reading

So na zuby is not about location here. It expresses purpose/use.

They mean different kinds of location.

• na stole = on the table
• v koupelně = in the bathroom

So:

• na is often used for something on a surface
• v is often used for something inside a space/place

That is why Czech says:

• na stole = on the table
• v koupelně = in the bathroom

This is very similar to English in this sentence.

Both are in the locative case, because they describe where something is.

• stůl = table

• na stole = on the table

• koupelna = bathroom
• v koupelně = in the bathroom

With location:

• na
  • locative = on
• v
  • locative = in

So here:

• stole is locative singular of stůl
• koupelně is locative singular of koupelna

This is different from motion:

• Je na stole. = It is on the table.
• Dám to na stůl. = I’ll put it on the table.

In the second sentence, na stůl is accusative because it shows movement toward a destination.

Because the negative form of je is není.

Czech usually makes verbs negative by adding ne-, but with být (to be), the forms are learned as complete words:

• je = is
• není = is not

So:

• Pasta na zuby je na stole. = The toothpaste is on the table.
• Pasta na zuby není na stole. = The toothpaste is not on the table.

You should learn není as the normal negative form, not as two separate words.

Because Czech often leaves out words that are already obvious from context.

The full version would be:

• Pasta na zuby není na stole, pasta na zuby je v koupelně.

But that sounds repetitive. Czech prefers the shorter version:

• Pasta na zuby není na stole, je v koupelně.

English usually needs the subject repeated:

• The toothpaste isn’t on the table, it’s in the bathroom.

Czech does this kind of omission very often, especially when the subject is clear.

Yes, but normally you would not say it unless you want emphasis or contrast.

Since pasta is feminine, you could say:

• Pasta na zuby není na stole, ona je v koupelně.

But this sounds more like:

• The toothpaste isn’t on the table; it is in the bathroom.

The pronoun ona adds emphasis and is usually unnecessary in a neutral sentence. The version without ona is more natural in ordinary speech.

Yes, Czech word order is flexible, but different orders change the emphasis.

The given sentence is neutral and natural:

• Pasta na zuby není na stole, je v koupelně.

Other possible versions:

• Pasta na zuby je v koupelně, ne na stole.
  This emphasizes the contrast more directly: in the bathroom, not on the table.

• V koupelně je pasta na zuby.
  This puts more focus on the location in the bathroom.

Czech word order often depends on what is already known and what is new or emphasized. The original sentence is a very standard, clear way to say it.

Yes. stole is the locative singular form of stůl (table).

The noun changes shape when it declines:

• nominative: stůl
• locative: (na) stole

This kind of stem change is normal in Czech and is something learners simply get used to over time.

So:

• stůl = table
• na stole = on the table

Because koupelna is a feminine noun, and after v for location it takes the locative singular form.

Basic pattern:

• koupelna = bathroom
• v koupelně = in the bathroom

Many feminine nouns in -a change to -ě in the locative singular after certain consonants.

For learners, the most important thing is to remember the whole phrase:

• v koupelně = in the bathroom

Yes, it is natural and understandable.

A native speaker might also say:

• Zubní pasta není na stole, je v koupelně.
• Pasta na zuby není na stole. Je v koupelně.

All of these are fine.

The main possible variation is pasta na zuby vs zubní pasta. Both work, but zubní pasta may sound a bit more standard to some speakers.

A simple approximate pronunciation is:

• Pasta na zuby není na stole, je v koupelně.
• PAH-sta na ZOO-bih NEH-nee na STO-le, ye v KOH-pehl-nyeh

A few details:

• z in zuby sounds like English z
• je sounds roughly like ye
• í is a long vowel
• ě in koupelně affects the sound of the preceding consonant, so ně sounds roughly like nye

You do not need a perfect accent at first; the most important thing is to keep the stress on the first syllable of each Czech word:

• PAs-ta
• ZU-by
• NE-ní
• STO-le
• KOU-pel-ně