Jedna kopia dokumentu leży na biurku.

Because kopia is a feminine noun, and jeden (one) has to agree with the noun in gender, number, and case.

So in the nominative singular:

• masculine: jeden
• feminine: jedna
• neuter: jedno

Since kopia is feminine, we say jedna kopia.

Kopia is in the nominative singular.

That is because it is the subject of the sentence — the thing that lies on the desk.

You can see this in the verb too:

• leży = lies / is lying
• it matches a third-person singular subject

So:

• Jedna kopia dokumentu = the subject
• leży = the verb
• na biurku = where it is

Because after kopia, Polish normally uses the genitive to express copy of something.

So:

• kopia dokumentu = a copy of a document / the document

Here:

• dokument is the dictionary form
• dokumentu is the genitive singular

This is a very common pattern in Polish:

• szklanka wody = a glass of water
• fragment tekstu = a fragment of a text
• kopia dokumentu = a copy of a document

It can mean either, depending on context.

Polish has no articles like a and the, so dokumentu by itself does not tell you whether the meaning is definite or indefinite.

So kopia dokumentu could be understood as:

• a copy of a document
• a copy of the document

The wider context tells you which is meant.

Because leżeć specifically means to lie or to be lying in a horizontal resting position.

So:

• leży na biurku = is lying on the desk
• jest na biurku = is on the desk

Both can be possible in some contexts, but leży gives a more concrete picture of the object physically resting there.

For objects like papers, books, documents, copies, and so on, leżeć is very natural.

Leży is the 3rd person singular present tense of leżeć.

So the present-tense forms are:

• leżę = I lie / am lying
• leżysz = you lie
• leży = he/she/it lies
• leżymy = we lie
• leżycie = you all lie
• leżą = they lie

In this sentence, the subject is singular:

• Jedna kopia → singular
• therefore leży

Because na can take different cases depending on meaning:

• na + accusative = movement onto something
• na + locative = location on something

Here there is no movement. The copy is already there, so we use the locative:

• na biurku = on the desk

Compare:

• Kładę dokument na biurko. = I put the document onto the desk.
• Dokument leży na biurku. = The document is lying on the desk.

Biurku is the locative singular of biurko.

The noun biurko is neuter, and after na meaning location, it goes into the locative:

• dictionary form: biurko
• locative singular: biurku

So:

• na biurku = on the desk

Yes, you could absolutely say Kopia dokumentu leży na biurku.

The difference is mainly one of emphasis:

• Kopia dokumentu leży na biurku. = A copy of the document is lying on the desk.
• Jedna kopia dokumentu leży na biurku. = One copy of the document is lying on the desk.

Using jedna highlights the number one a bit more. Sometimes it contrasts with other copies, even if that contrast is only implied.

Yes. Polish word order is more flexible than English word order.

The neutral order here is:

• Jedna kopia dokumentu leży na biurku.

But other orders are possible for emphasis, for example:

• Na biurku leży jedna kopia dokumentu.
  This puts more focus on where it is.
• Jedna kopia dokumentu na biurku leży.
  Grammatically possible, but much less natural in normal speech.

So the original sentence is a very natural, neutral way to say it.

Because Polish does not have articles.

English distinguishes:

• a copy
• the copy

Polish usually just says:

• kopia

Whether it means a or the depends on context.

That is why a short Polish sentence can look more compact than its English equivalent.

Here are the basic dictionary forms:

• jeden = one
• kopia = copy
• dokument = document
• leżeć = to lie / to be lying
• biurko = desk

And the forms used in the sentence are:

• jedna ← from jeden
• kopia ← dictionary form unchanged
• dokumentu ← from dokument
• leży ← from leżeć
• biurku ← from biurko

A simple approximate pronunciation is:

YED-nah KOH-pyah doh-koo-MEN-too LEH-zhih nah byOOR-koo

A few useful notes:

• je in jedna sounds roughly like ye
• ko in kopia is like ko in coffee, but shorter
• ży in leży has the ż sound, like the s in measure
• biurku begins with a sound like byur-

Stress in Polish usually falls on the second-to-last syllable:

• JED-na
• KO-pia
• dokuMENtu
• LEży
• biurKU

It is built by normal grammar, but it is also a very common combination.

Polish often links two nouns by putting the second one in the genitive:

• numer telefonu = phone number
• kolor ściany = the color of the wall
• kopia dokumentu = copy of a document

So this is not an idiom you just memorize as a special exception. It follows a productive pattern that you will see often.