Learn Croatian: Nema dosta brašna. - There is not enough flour.

It is in the genitive case! In this lesson, we learn that indefinite quantifiers like dosta (enough), malo (a little), and puno (a lot) must be followed by the noun in the genitive case. Since brašno is a neuter noun, it takes the -a ending in the genitive singular.

Why do we use Nema to mean "there is not"? Doesn't that mean "he/she/it does not have"?

Yes, nema is the "he/she/it" form of nemati (to not have). However, Croatian commonly uses ima (it has) and nema (it does not have) to mean "there is" and "there is not".

If I remove dosta, how do I say "There is no flour"?

You would just say Nema brašna. Interestingly, the word nema (when used to mean "there is no") also requires the genitive case! So whether it's triggered by the quantifier dosta or by the verb nema, brašno must change to brašna.

I've seen dosta used to mean "a lot". How do I know it means "enough" here?