Svaka presadnica treba dovoljno vode.

Because presadnica is a feminine singular noun, and svaki/svaka/svako must agree with the noun in gender, number, and case.

Here the subject is:

• svaka = every, each (feminine singular nominative)
• presadnica = seedling/transplant (feminine singular nominative)

Compare:

• svaki cvijet = every flower (masculine)
• svaka presadnica = every seedling (feminine)
• svako dijete = every child (neuter)

It is in the nominative singular because it is the subject of the sentence.

The structure is:

• Svaka presadnica = the subject
• treba = the verb
• dovoljno vode = what it needs

So presadnica stays in the nominative because it is the thing doing the needing.

Because the subject svaka presadnica is grammatically singular.

Even though svaka refers to all seedlings one by one, Croatian treats svaka presadnica as each individual seedling, so the verb is singular:

• Svaka presadnica treba... = Each seedling needs...
• not trebaju

If the subject were plural, then the verb would be plural:

• Presadnice trebaju dovoljno vode. = Seedlings need enough water.

Because dovoljno usually requires the genitive case.

So:

• dovoljno vode = enough water

Here vode is genitive singular of voda.

This is very common in Croatian after words of quantity:

• puno vode = a lot of water
• malo vremena = a little time
• dosta novca = enough / plenty of money

If you remove dovoljno, then you would normally use the regular direct object:

• Presadnica treba vodu. = The seedling needs water.

So the difference is:

• treba vodu = needs water
• treba dovoljno vode = needs enough water

Here dovoljno functions as a quantity word, roughly like enough.

It does not behave like a normal adjective agreeing with the noun. Instead, it stays in the same form and is followed by a genitive noun:

• dovoljno vode
• dovoljno sunca
• dovoljno vremena

So in this sentence, think of dovoljno vode as a unit meaning enough water.

Because trebati can be used in more than one way in Croatian.

Here it means to need:

• Presadnica treba vodu. = The seedling needs water.

But treba can also appear in expressions meaning it is necessary / one should, especially with an infinitive:

• Treba zalijevati biljke. = One should water the plants. / It is necessary to water the plants.

So in your sentence, treba is a normal lexical verb meaning needs, not a modal meaning should.

Yes, that is grammatical, but it means something slightly different.

• Svaka presadnica treba vodu. = Every seedling needs water.
• Svaka presadnica treba dovoljno vode. = Every seedling needs enough water.

The second sentence is more specific because it talks about a sufficient amount.

Yes. Croatian word order is fairly flexible, although the neutral order here is very natural:

• Svaka presadnica treba dovoljno vode.

You can move things around for emphasis, for example:

• Dovoljno vode treba svaka presadnica.
  Emphasizes enough water.

• Treba svaka presadnica dovoljno vode.
  Grammatically possible in some contexts, but less neutral and less likely as a basic sentence.

For learners, the original order is the best one to use first.

Yes. Presadnica is a normal countable noun.

You can say:

• jedna presadnica = one seedling
• dvije presadnice = two seedlings
• tri presadnice = three seedlings

That is why svaka presadnica works naturally: svaka is used with singular countable nouns to mean each/every.

The dictionary forms are:

• svaki = every, each
• presadnica = seedling, transplant
• trebati = to need
• dovoljno = enough
• voda = water

In the sentence, some of these appear in forms required by grammar:

• svaki → svaka to match the feminine noun
• voda → vode because it follows dovoljno

A natural plural version would be:

• Presadnice trebaju dovoljno vode. = Seedlings need enough water.

Notice the changes:

• presadnica → presadnice (plural subject)
• treba → trebaju (plural verb)

You would usually not say svake presadnice trebaju... unless you specifically want all seedlings / each of the seedlings in a particular context. The singular with svaka is the normal way to say every seedling.