La popa, desde donde vimos el mar, estaba vacía.

La popa means the stern or the back part of a ship/boat.

A few related nautical words:

• la proa = the bow, the front of the ship
• babor = port side
• estribor = starboard side

It is a feminine noun, so it takes la:

• la popa
• la popa estaba vacía

In Spanish, articles are used more often than in English. So where English might sometimes say stern, Spanish will usually say la popa.

Here it refers to a specific stern: the stern of the ship being talked about. That is why la sounds natural.

Desde donde means from where.

In this sentence:

• desde donde vimos el mar = from where we saw the sea

It introduces a place connected to la popa:

• La popa = the place
• desde donde vimos el mar = from which place we saw the sea

A more literal breakdown:

• desde = from
• donde = where

Because here donde is a relative word, not a question word.

Compare:

• ¿Dónde vimos el mar? = Where did we see the sea?
  → question, so it has an accent: dónde

• La popa, desde donde vimos el mar, estaba vacía.
  → not a question; it means from where, linking back to la popa, so no accent: donde

A useful rule:

• dónde = in direct or indirect questions
• donde = in relative clauses

Because that part is extra information about la popa. It is a non-essential relative clause.

The main sentence is:

• La popa estaba vacía. = The stern was empty.

The middle part:

• desde donde vimos el mar just adds extra detail:
• the stern, from where we saw the sea, was empty

The commas show that the speaker is pausing to insert additional information.

This is a very common Spanish tense contrast:

• vimos = preterite
• estaba = imperfect

Why?

vimos

Vimos presents the action of seeing the sea as a completed event:

• we saw the sea

It is something that happened.

estaba

Estaba describes the condition/state of the stern:

• it was empty

The imperfect is often used for background description, states, and circumstances.

So the contrast is:

• vimos = completed action
• estaba = background description/state

This is very natural in Spanish narration.

Because Spanish often leaves out subject pronouns when the verb form already makes the subject clear.

• vimos already tells you the subject is we
• so nosotros vimos is possible, but usually unnecessary

So:

• desde donde vimos el mar naturally means
• from where we saw the sea

In Spanish, mar usually appears with an article:

• el mar = the sea

So:

• vimos el mar = we saw the sea

A cultural note:

• el mar is the standard form
• la mar also exists, but it is more poetic, literary, or regional

For most learners, el mar is the normal choice.

Yes. These are possible alternatives.

For example:

• La popa, desde la que vimos el mar, estaba vacía.
• La popa, desde la cual vimos el mar, estaba vacía.

These also mean roughly the stern, from which we saw the sea, was empty.

Differences:

• desde donde sounds very natural and straightforward for places
• desde la que is also natural
• desde la cual is a bit more formal or written

So desde donde is a good, idiomatic choice.

Vacía agrees with la popa, which is:

• feminine
• singular

So the adjective must also be:

• feminine
• singular

That is why it is:

• vacía

Compare:

• el barco estaba vacío = the ship was empty
• la popa estaba vacía = the stern was empty
• las cabinas estaban vacías = the cabins were empty

The accent mark shows the stress and also helps indicate that í-a is pronounced in two syllables:

• va-cí-a

So it is not pronounced as one smooth syllable like vacia would be.

This happens in many words where a weak vowel like i or u is stressed next to another vowel:

• vacía
• día
• frío
• país

The core structure is:

• La popa = subject
• estaba = verb
• vacía = adjective/complement

So the main sentence is:

• La popa estaba vacía.

Then the relative phrase is inserted:

• desde donde vimos el mar

So the full structure is:

• La popa,
  desde donde vimos el mar,
  estaba vacía.

This is similar to English:

• The stern, from where we saw the sea, was empty.

Yes, it is grammatical and natural.

That said, depending on style, some speakers might prefer slightly different versions, such as:

• La popa, desde la que vimos el mar, estaba vacía.
• La popa, desde la cual vimos el mar, estaba vacía.

But desde donde is perfectly normal, especially when referring to a place.

So for a learner, the sentence is a good example of:

• a place noun
• a relative clause with donde
• preterite vs imperfect
• adjective agreement