As the linked Daily Camera article says, the students are already "locked into the costs of their meal plans". The dining halls are, essentially, all-you-can-eat (and drink) buffets:

"As it stands, students can treat the three campus dining halls as all-you-can buffets, meaning they can fill up on sodas and sugary juices to their hearts' content."

The tax is paid by CU to the drink vendor. CU puts the "sugary" drinks in the same place / fountain as all of the other choices. Students come in and get whatever drink they want, as much as they want.

Apart from segregating the newly-taxed beverages and having the meal-plan students pay cash every time they fill up with those choices, how would CU raise the prices on just those drinks, without raising all beverage prices?

A previous comment used McDonald's as an example: since a single fountain dispenses both sugary and non-sugary beverages, how would McDonald's charge different prices for the two beverage types?