Molim te, dodaj malo limuna u vodu.

Molim is the 1st person singular present of moliti (to ask / to beg / to request), so literally it’s I’m asking. In polite requests, Croatian often uses Molim as a set phrase meaning please.
te is the accusative (direct object) clitic form of ti (you, informal singular). So Molim te is literally I’m asking you → idiomatically Please.

Yes. Molim by itself can work as please (especially in more formal or neutral contexts).

• Molim, dodaj... = polite, slightly more neutral
• Molim te, dodaj... = a bit more personal/direct because it explicitly addresses you (informal)

dodaj is the imperative (command/request) form of dodati (to add), addressed to ti (informal singular): (you) add.
dodaješ is present tense (you add / you are adding) and would not be the normal form for a request.

You change both the pronoun and the imperative form:

• Informal singular: Molim te, dodaj...
• Formal singular / plural (Vi): Molim Vas, dodajte...
• Informal plural (vi): Molim vas, dodajte...

So the formal version is: Molim Vas, dodajte malo limuna u vodu.

Here malo means a little (bit) of and functions like a quantity word. It doesn’t describe the noun as an adjective (small lemon), but expresses an amount: a little lemon (i.e., a small amount of lemon/juice).
That’s why you get malo + genitive (see next question).

Because malo (in the sense of a little of) commonly requires the genitive: malo + genitive.

• limun = nominative (basic dictionary form)
• limuna = genitive singular (or genitive used for “some/amount of”)

So malo limuna = a little (bit) of lemon.

It’s intentionally vague. It can mean:

• a bit of lemon juice
• a small amount of lemon (e.g., squeezed lemon)
• sometimes even a few small pieces/slices, depending on context

If you want to be specific, you can say:

• malo limunovog soka = a little lemon juice
• krišku limuna / dvije kriške limuna = a slice / two slices of lemon

With u:

• u + accusative expresses motion/adding into (direction): into the water
• u + locative expresses location: in the water

Since you’re putting lemon into the water, it’s u vodu (accusative).
If you were describing something already inside, you’d say u vodi.

vodu is the accusative singular of voda. The preposition u (meaning into) requires the accusative here, so voda → vodu.

Croatian word order is fairly flexible, but clitics like te usually stay near the beginning (often in the 2nd position of the clause). Common natural options:

• Molim te, dodaj malo limuna u vodu. (neutral)
• Molim te, dodaj u vodu malo limuna. (focus on “into the water”)
• Molim te, u vodu dodaj malo limuna. (more emphasis, slightly marked)

The most “standard” is the original.

dodati is typically perfective: adding once/a specific amount (a complete action). That fits a single request: add (some) lemon.
dodavati is imperfective and would suggest an ongoing/repeated action or process. In a kitchen/drink context you could hear:

• Dodaj malo limuna... = add a bit (once)
• Dodavaj malo limuna... = keep adding a bit (gradually), or add repeatedly (less common as a simple request)

Approximate pronunciation (stress varies by dialect, but this will be understood):
MO-lim te, DO-daj MA-lo LI-mu-na u VO-du.
Notes:

• j is like English y in yes
• u is like oo in food (shorter)
• č/ć/š/ž aren’t in this sentence, so it’s fairly straightforward.