Having lowered his own British record on Saturday in the 50m freestyle, the Plymouth Leander star set a new BUCS record in the two-length event on Sunday.
University of St Mark and St John student Proud clocked 49.10 seconds to claim victory, which was more than a second ahead of second-placed Jack Thorpe of Edinburgh, who touched in 50.57.
Proud’s university team-mate John Slater was seventh in the same final with a time of 52.57.
Leander’s Perry Gardener, who won the 200m backstroke on Saturday, just missed out on another medal on Sunday with a fourth-placed finish in the 100m backstroke.
Gardener clocked 57.14 seconds, with team-mate Adam Milner ninth in 59.10.
Plymouth’s Belgium international Juliette Casini was sixth in the women’s 100m freestyle in 57.38, while former Plymouth College star Charlotte Atkinson, now at Loughborough University, won the 200m butterfly final and came second in the 50m butterfly event on Sunday.