Když vařím rýži, dávám do ní sůl a pepř.

Here když means when.

In this sentence, Když vařím rýži... means When I cook rice... or more naturally Whenever I cook rice... because the whole sentence describes a habitual action.

Czech když is often used for:

• when: Když přijdu domů, jím. = When I come home, I eat.
• sometimes conversational if, but in standard learning contexts it is best to think of it primarily as when

So in your sentence, it introduces a time clause:

• Když vařím rýži = When/Whenever I cook rice

Czech uses the present tense here because this sentence expresses a general habit or repeated action.

So:

• vařím = I cook / I am cooking
• dávám = I put / I add / I am putting

In English, we also often use the present simple for habits:

• When I cook rice, I add salt and pepper.

Czech does the same thing. It is not describing one specific cooking event unless the context makes that clear. By itself, it sounds like a regular habit.

Vařím is the 1st person singular present form of the verb vařit = to cook.

So:

• vařit = to cook
• vařím = I cook / I am cooking

This verb is imperfective, which fits well here because the sentence talks about an ongoing or habitual activity, not a single completed act.

Some present-tense forms of vařit:

• vařím = I cook
• vaříš = you cook
• vaří = he/she/it cooks
• vaříme = we cook
• vaříte = you cook
• vaří = they cook

Because rýže is the direct object of vařím, so it has to be in the accusative case.

• rýže = nominative singular
• rýži = accusative singular

In the sentence:

• vařím rýži = I cook rice

This is very common in Czech: the thing directly affected by the verb often goes into the accusative.

Literally, dávat often means to give, but in many contexts it also means to put.

Here:

• dávám do ní sůl a pepř = I put/add salt and pepper into it

So the natural English translation is:

• I add salt and pepper to it or
• I put salt and pepper in it

In cooking contexts, dávat is very often used for putting ingredients into something.

This is a question of aspect.

• dávat = imperfective = ongoing, repeated, habitual
• dát = perfective = single completed act

Since the sentence describes what you usually do when cooking rice, Czech uses the imperfective:

• dávám = I add / I usually put

If you said dám, it would sound more like a single completed action in a specific situation, not a general habit.

So:

• Když vařím rýži, dávám do ní sůl a pepř. = habitual
• Dám do ní sůl a pepř. = I’ll put salt and pepper in it / I put it in once

Do ní means into it.

It is made of:

• do = into
• ní = her/it, after a preposition

Here ní refers to rýže, which is a feminine noun in Czech.

Czech often uses a preposition + pronoun where English might simply use it or to it:

• do ní = into it
• literally: into her/it

So:

• dávám do ní sůl a pepř = I put/add salt and pepper into it

Because it refers back to rýže, and rýže is grammatically feminine in Czech.

In Czech, pronouns agree with the grammatical gender of the noun they refer to.

So:

• rýže = feminine
• therefore ní is the feminine form

This is grammatical gender, not biological gender. Foods and objects can be masculine, feminine, or neuter in Czech, and pronouns match that grammatical category.

The preposition do requires the genitive case.

So after do, the pronoun must be in the genitive form:

• ona / to type reference to a feminine noun
• after do → do ní

That is why you get:

• do ní = into it

Similarly:

• do domu = into the house
• do školy = into the school
• do ní = into it

They are in the accusative case because they are the direct objects of dávám.

You are putting what into the rice?

• sůl a pepř

So they function as direct objects.

In this sentence, their accusative forms happen to look the same as their dictionary forms:

• sůl = salt
• pepř = pepper

That is normal. In Czech, some nouns have the same form in nominative and accusative.

Because Czech has no articles.

English says:

• the rice
• salt
• pepper
• a pepper etc.

Czech usually expresses definiteness from context, not with separate words like the or a.

So:

• rýži can mean rice / the rice
• sůl a pepř can mean salt and pepper

You simply understand from the situation what is meant.

Because Když vařím rýži is a subordinate clause, and Czech normally separates subordinate clauses from the main clause with a comma.

So:

• Když vařím rýži, dávám do ní sůl a pepř.

This is standard Czech punctuation.

A good rule for learners:

• If a sentence begins with když, že, protože, jestli, and similar conjunctions, there is often a comma separating the clause from the rest of the sentence.

Yes, it can suggest that too, depending on context.

Because both verbs are imperfective and in the present tense, the sentence can naturally cover:

• When I cook rice, I add salt and pepper to it = habitual meaning
• While I’m cooking rice, I add salt and pepper to it = process meaning

Without extra context, the most natural interpretation is the habitual one: Whenever I cook rice, I add salt and pepper.

Do ní is perfectly natural, but there are other ways Czech speakers might express the idea.

For example:

• Když vařím rýži, dávám do ní sůl a pepř.
• Když vařím rýži, přidávám do ní sůl a pepř.
• Když vařím rýži, solím ji a pepřím ji. — less neutral, more like I salt and pepper it

A very common alternative is přidávat:

• přidávám = I add

But your original sentence with dávám do ní is absolutely normal and understandable.

The basic structure is:

• Když vařím rýži = subordinate clause
• dávám do ní sůl a pepř = main clause

Word order in Czech is more flexible than in English, but not random. The original sentence sounds natural and neutral.

You could also hear variations like:

• Když vařím rýži, dávám do ní pepř a sůl.
• Sůl a pepř dávám do ní, když vařím rýži. — grammatically possible, but more marked and less neutral

For learners, the given word order is a very good standard model.