Se eu estiver com dor na garganta, vou beber água com limão.

Because after se when you are talking about a possible future condition, Portuguese normally uses the future subjunctive, not the present indicative.

So:

• Se eu estiver com dor na garganta... = if I am / if I happen to be with a sore throat
• Se eu estou... sounds wrong in this kind of future condition

A useful pattern is:

• Se eu estiver...
• Se ele tiver...
• Se nós formos...

This is one of the most important uses of the future subjunctive in Portuguese.

Estiver is the future subjunctive form of estar.

In this sentence, it means something like if I am in a future or hypothetical situation.

A few examples:

• Se eu estiver cansado, vou dormir cedo.
• Se ela estiver em casa, eu ligo.

One important detail: estiver is the same form for eu and ele/ela/você.

• se eu estiver
• se você estiver
• se ela estiver

Portuguese often expresses temporary physical conditions with estar com + noun.

So estar com dor literally means to be with pain, but idiomatically it means to have pain.

Very common examples:

• estar com febre = to have a fever
• estar com sono = to be sleepy
• estar com dor de cabeça = to have a headache
• estar com dor na garganta = to have pain in the throat

This is a very natural Portuguese structure, even if it feels different from English.

Na is a contraction of:

• em
  • a = na

So:

• na garganta = in the throat / in my throat

Since garganta is a feminine noun, em a garganta becomes na garganta.

Other similar contractions:

• no = em + o
• nos = em + os
• nas = em + as

Examples:

• no braço = in the arm
• na cabeça = in the head
• nas costas = in the back

Yes, but the difference is small.

• dor na garganta = pain in the throat
• dor de garganta = sore throat / throat pain as a condition

In everyday Brazilian Portuguese, both are understood and both can sound natural.

A rough way to think about it:

• dor na garganta focuses a little more on the location of the pain
• dor de garganta is a very common fixed expression for sore throat

So this sentence is fine, but many Brazilians might also say:

• Se eu estiver com dor de garganta, vou beber água com limão.

Vou beber is the very common ir + infinitive future, similar to English going to drink.

In spoken Brazilian Portuguese, this is usually more natural than the simple future:

• vou beber = very common in everyday speech
• beberei = correct, but often sounds more formal, literary, or less conversational

So in normal conversation, Brazilians often prefer:

• vou fazer
• vou comer
• vou beber

instead of:

• farei
• comerei
• beberei

Yes, you often can, if the subject is clear from context.

Portuguese frequently drops subject pronouns, so these can both work:

• Se eu estiver com dor na garganta, vou beber água com limão.
• Se estiver com dor na garganta, vou beber água com limão.

Including eu can make the sentence a little clearer or more explicit. After se, keeping the pronoun is very normal.

So:

• with eu = clear and standard
• without eu = also natural when the subject is obvious

Because the sentence starts with a conditional clause:

• Se eu estiver com dor na garganta = condition
• vou beber água com limão = main clause

In Portuguese, when this kind of if clause comes first, a comma is normally used.

So:

• Se eu estiver com dor na garganta, vou beber água com limão.

If you reverse the order, the comma is often not used:

• Vou beber água com limão se eu estiver com dor na garganta.

No. Água com limão means water with lemon.

That could mean:

• water with lemon juice
• water with a slice of lemon
• warm water with lemon

If you want lemonade, the usual word is:

• limonada

So:

• água com limão ≠ lemonade
• limonada = lemonade

Yes. Both are natural.

• beber água com limão
• tomar água com limão

In Brazilian Portuguese, tomar is very common for drinks, medicine, and similar things. Beber is also completely correct and natural.

Very roughly:

• beber focuses more directly on the act of drinking
• tomar is broader and extremely common in everyday speech

So this version is also fine:

• Se eu estiver com dor na garganta, vou tomar água com limão.

It usually suggests a real or possible future situation.

The structure:

• Se eu estiver..., vou...

often means If this happens, then I’ll do that.

So it sounds like a plan or response:

• if I have a sore throat, I’ll drink water with lemon

It is not necessarily very doubtful or imaginary. It can be a perfectly realistic condition.

Yes, it sounds natural.

A Brazilian speaker might also say slightly different versions, such as:

• Se eu estiver com dor de garganta, vou beber água com limão.
• Se eu ficar com dor de garganta, vou tomar água com limão.

These are just variations:

• estar com dor = to be with pain / to have pain
• ficar com dor = to end up getting pain / to come down with it
• beber and tomar are both fine

So the original sentence is good Portuguese.