1. Drink more than three 300-milliliter bottles of water every day.

2. Drink over 0.5-milliliter of bottles of water a day.

3. Drink three 0.5-ml of bottles of water every day.

4. Drink three one-liter bottles of water a day.
(Can we use all the expressions?)

2 answers

1. 3 * 300ml = 3 * .3 liters = .9 liters

2 and 3 are even less, but 2 = .005 liters, 3 = .015 liters

4. is a possibility, but that is too much water.

It would be better to express all in liters, but you would want them to drink more than .0015 liters a day.
PsyDAG is right about the amounts of water. Try these:

Drink more than three half-liter bottles of water a day.

Drink more than two liters of water a day.

The simpler you can make the phrasing, the easier it will be for others to understand.