These constructions are called "mass nouns" (or something comparable). Although they refer to more than one thing (e.g., more than one milliliter of water), they treat these things as a single unit.
Mass nouns take singular verbs - not plural (reference and reference).
Take your first example:
I took 2 ml of water, which was/were then added...
The water, despite being more than one milliliter, was added at the same time, as a single unit. It would not be helpful (semantically or grammatically) to think of each milliliter of water as being added separately. Instead, treat the mass noun as the group it is, and use the singular.