Psychology student Ben Cronin, 20, alleges that he was shocked when staff told him he wasn't attractive enough to work the boats on the River Cam.
Mr Cronin, who has just completed his first year at Anglia Ruskin University in Cambridge, had hoped to fund his second year of studies by working on the water.
But after his rejection he now faces a summer of bar work, he said.
Staff at the punting company deny making the comments.
"I was with a couple of friends and we decided to go and speak to one of the punting companies to see if we could get work for the coming season,” Mr Cronin said. “I went to speak to the man running the boats, but when I asked about a job, he looked me up and down and laughed, saying: 'Sorry mate, you have to be good looking to do this job.' I wanted the ground to swallow me up. I felt so humiliated.
"This guy was tall, dark and good looking. I've been punting a few times and am sure that I could do the job. I don't see what the way I look has to do with getting the job. The way he spoke to me has put me off wanting to punt on the river ever again. It was so embarrassing. It's had a huge effect on my self esteem.”
The student has since complained to nearby punting company Scudamore's. The company has begun an investigation, but staff say they do not recognize the description given as a member of their team.
Rod Ingersent, general manager of Scudamore's, said: "The alleged comment is not something we endorse, as we recruit purely on the basis of work criteria and individual merit."