Hava güzel, ne var ki su çok soğuk.

Here ne var ki means however, but, and yet, or the thing is. It introduces a contrast between the two clauses:

• Hava güzel = the weather is nice
• ne var ki su çok soğuk = however, the water is very cold

It is a slightly more formal or literary way to express contrast than plain ama.

In this sentence, it is best learned as a fixed expression.

Literally, the parts are:

• ne = what
• var = there is / exists
• ki = a linking particle

But in real usage, ne var ki functions together as a discourse connector meaning however / unfortunately / still.

So although you can analyze the pieces, learners should mainly recognize it as one expression.

Turkish often uses nominal sentences in the present tense without an overt verb like is.

So:

• Hava güzel literally looks like weather nice
• but it means The weather is nice

The same thing happens in:

• Su çok soğuk = The water is very cold
• O mutlu = He/She is happy
• Ev büyük = The house is big

In the simple present, Turkish often leaves out to be.

These mean different things.

• Su çok soğuk = The water is very cold
  Here soğuk is the predicate adjective describing su.

• çok soğuk su = very cold water
  Here it is a noun phrase, not a full sentence.

So in your sentence, su çok soğuk is a complete clause: subject + description.

Because çok means very here, and in Turkish it comes before the adjective it modifies:

• çok güzel = very beautiful / very nice
• çok soğuk = very cold
• çok sıcak = very hot

So:

• su çok soğuk = the water is very cold

This is similar to English word order with very cold.

Turkish has no definite article like English the.

So:

• hava can mean air or the weather, depending on context
• su can mean water or the water

In this sentence, context makes them definite and specific:

• Hava güzel = The weather is nice
• su çok soğuk = the water is very cold

Turkish relies heavily on context where English uses the.

Here it means weather.

The word hava can mean both air and weather, but in common everyday sentences like:

• Hava güzel
• Hava soğuk
• Hava bugün çok sıcak

it usually means the weather.

Yes. The sentence could also be said as:

• Hava güzel ama su çok soğuk.
• Hava güzel fakat su çok soğuk.
• Hava güzel, ancak su çok soğuk.

These all express contrast, but the nuance is a little different:

• ama = the most common everyday but
• fakat = a bit more formal
• ancak = formal or written
• ne var ki = somewhat literary, expressive, or slightly stronger in tone

So ne var ki is perfectly correct, but not the most basic everyday choice.

Because in ne var ki, ki is a separate conjunction/particle, not a suffix.

This is important because Turkish also has a different -ki that attaches to the previous word, as in:

• evdeki = the one in the house / the one at home
• dünkü = yesterday’s

But in your sentence:

• ne var ki

the ki is written separately because it is part of the fixed connector expression.

Yes, but it is understood rather than shown with a separate verb.

Both clauses are in the simple present:

• Hava güzel = The weather is nice
• su çok soğuk = The water is very cold

Turkish often leaves the present-tense form of to be unspoken in this kind of sentence.

Soğuk is pronounced roughly like so-uk, with a soft transition between the vowels.

The letter ğ in Turkish usually does not sound like a hard consonant. It often:

• lengthens the previous vowel, or
• creates a smooth glide between vowels

So soğuk is not pronounced with a strong g sound. It is closer to:

• so-uk
• or soo-uk

depending on accent and speech speed.

A rough pronunciation of the whole sentence is:

• Hava güzel, ne var ki su çok soğuk
• HA-va gü-ZEL, ne var ki su chok so-uk

The comma is natural and helpful, because ne var ki links two contrasting clauses.

So this punctuation is very normal:

• Hava güzel, ne var ki su çok soğuk.

In informal writing, some people may omit the comma, but with a connector like ne var ki, the comma makes the structure clearer.

Yes, it is correct and natural, especially in writing or slightly more polished speech.

That said, many speakers in everyday conversation would more commonly say:

• Hava güzel ama su çok soğuk.

So your sentence is natural, but ne var ki sounds a bit more formal, literary, or stylistically marked than ama.