Eu prefiro água com limão quando estou com dor de garganta.

Yes, Portuguese often leaves out subject pronouns because the verb ending already shows the subject. So:

• Prefiro água com limão... = perfectly natural
• Eu prefiro água com limão... = also natural

Including eu can add:

• emphasis: I prefer...
• contrast: Eu prefiro água com limão, mas ela prefere chá.
• a slightly clearer, more explicit tone

So in this sentence, eu is optional, not required.

Prefiro is the 1st person singular present of preferir (to prefer).

Conjugation:

• eu prefiro = I prefer
• você prefere = you prefer
• ele/ela prefere = he/she prefers
• nós preferimos = we prefer
• eles/elas preferem = they prefer

So Eu prefiro... simply means I prefer...

Both are possible, but they can sound slightly different depending on context.

• Eu prefiro água com limão... = I prefer water with lemon, in a general sense
• Eu prefiro a água com limão... = I prefer the water with lemon, or lemon water as a more specific option

In general statements, Portuguese often omits the article with foods and drinks:

• Eu bebo café.
• Ela come arroz.
• Eu prefiro água com limão.

So the version without the article sounds very natural here.

The word is spelled água with an acute accent because the stress falls on the first syllable: Á-gua.

The accent helps show the correct stress pattern. Without it, the spelling would not follow normal Portuguese stress rules.

Also note:

• água is a feminine noun
• you say a água
• but because of pronunciation, it takes the masculine-looking article form a, not uma issue? Actually:
  • a água
  • uma água

The important point is: água is feminine, even though it starts with a stressed a sound.

Both can exist, but they do not always mean the same thing.

• água com limão = water with lemon added to it
• água de limão can sound more like lemon-flavored water or a more fixed drink name, depending on context

In everyday Brazilian Portuguese, água com limão is the most natural way to say water with lemon in this situation.

Compare:

• chá com limão = tea with lemon
• água com gás = sparkling water
• pão com manteiga = bread with butter

In Brazil, limão can refer to fruits that English speakers may call either lemon or lime, depending on the variety.

So this can be a little tricky. In everyday Brazilian usage:

• limão is the normal general word
• if needed, people specify the type:
  • limão-taiti
  • limão-siciliano
  • etc.

So in translation, limão may become lemon in English, but the exact fruit type can depend on context.

Because estar is used for temporary states or conditions, while ser is used for more permanent identity or characteristics.

Here, the speaker means:

• when I am / when I’m feeling / when I have a sore throat

That is a temporary condition, so Portuguese uses estar:

• quando estou com dor de garganta

Using ser here would be incorrect.

Literally, it means something like:

• I am with throat pain

But natural English is:

• I have a sore throat
• I have throat pain

This is a very common Portuguese structure:

• estar com fome = to be hungry / literally to be with hunger
• estar com sede = to be thirsty
• estar com sono = to be sleepy
• estar com dor de cabeça = to have a headache
• estar com dor de garganta = to have a sore throat

So estar com is often used where English uses to have.

Yes, Tenho dor de garganta is understandable and correct. It means I have a sore throat.

But in everyday Brazilian Portuguese, estou com dor de garganta often sounds more natural when talking about a current temporary condition.

Compare:

• Estou com dor de garganta. = I currently have a sore throat.
• Tenho dor de garganta. = also correct, but can sound a little less conversational in some contexts.

Both are used; estou com is just very common for temporary symptoms.

Both exist, but they are used a little differently.

• dor de garganta = sore throat / throat pain as a condition or symptom
• dor na garganta = pain in the throat, often focusing more on the location

So:

• Estou com dor de garganta = I have a sore throat
• Sinto dor na garganta = I feel pain in my throat

In your sentence, dor de garganta is the standard expression.

Yes, somewhat. The original sentence is very natural:

• Eu prefiro água com limão quando estou com dor de garganta.

You could also say:

• Quando estou com dor de garganta, eu prefiro água com limão.

Both are correct. The difference is mostly emphasis:

• starting with Eu prefiro... emphasizes the preference
• starting with Quando estou com dor de garganta... emphasizes the situation

A rough pronunciation guide is:

• Eu ≈ eh-o / often closer to yo depending on accent
• prefiro ≈ preh-FEE-roo
• água ≈ AH-gwa
• com ≈ kong or kohm depending on accent
• limão ≈ lee-MOWN
• quando ≈ KWAN-doo
• estou ≈ es-TOH or is-TOH
• com dor ≈ kong dor
• de garganta ≈ jee gar-GAN-ta in many Brazilian accents, because de often sounds like jee before some sounds in casual speech? More carefully here it is closer to djee or dee, depending on accent.

A more natural Brazilian rhythm would connect words a lot:

• Eu prefiroágua com limão quandoestou com dor de garganta.

The most important stress points are:

• preFIro
• Água
• liMÃO
• QUANdo
• esTOU
• garGANta

The sentence uses the present tense:

• prefiro = I prefer
• estou = I am

But the meaning is a general habit or usual preference, not only something happening exactly right now.

So:

• Eu prefiro água com limão quando estou com dor de garganta. means something like:
• I prefer water with lemon when I have a sore throat.

This is a very common use of the present tense in both Portuguese and English.

Yes, but it changes the meaning slightly.

• Eu prefiro água com limão... = I prefer water with lemon...
• Eu gosto mais de água com limão... = I like water with lemon more...

Preferir is the cleaner and more direct verb for expressing preference between options. It is usually the best choice here.

Also note:

• with gostar, you need de
  • Eu gosto de água com limão.
• with preferir, you do not use de
  • Eu prefiro água com limão.

Because dor de garganta is a fixed expression, similar to a symptom name.

In many Portuguese noun phrases with de, the second noun appears without an article:

• dor de cabeça
• dor de dente
• suco de laranja
• copo de água

So garganta does not need a here.

If you say na garganta, then you are using a different structure:

• Sinto dor na garganta. = I feel pain in my throat.

Yes, very natural. A Brazilian would easily say:

• Eu prefiro água com limão quando estou com dor de garganta.

Other natural alternatives include:

• Quando estou com dor de garganta, prefiro água com limão.
• Eu gosto de tomar água com limão quando estou com dor de garganta.

But your original sentence sounds completely normal and idiomatic.