Deep cuts, Bowles warns, could be disastrous for the 16 public universities that comprise the UNC system.
Bowles has expressed great concern for students who depend on financial assistance and those who depend on the universities for work.
However, students are still feeling the impact of last year's budget cuts.
"A lot of classes get cut," UNC Chapel Hill student Sarah Smith said. "They only offer them spring or fall semester."
Things could get worse according to Bowles, if state lawmakers won't budge on their budget plan, which calls for nearly $240 million in cuts.
He warns that it could be hard for the UNC system to recover. It has already lost key faculty members to competing schools offering more money.
Hundreds of jobs would also be in jeopardy and students would see a significant reduction in classes and financial aid.
"It does help out my family to have someone help pay for my college," UNC Chapel Hill student Maryam Amnda said.
But even some scholarship programs are at risk of being cut.
Extended library hours are also on the chopping block.
Bowles admits these are tough times that require tough decisions, but not at the expense of students.
The budget crisis may also force more students to delay graduation beyond four years.
"We're all students, they need to remember how our families can be affected," Amnda said.
Bowles says he and other university leaders will try to lobby lawmakers to make changes that would save jobs and financial aid for students in need.