Morales attended Bellarmine College Preparatory, in San Jose, California, and trained under the supervision of Larry Rogers.

At the trials, Morales also set relay records with teammates Rick Carey, Steve Lundquist and Rowdy Gaines.

After losing the 100-meter butterfly world record to German swimmer Michael Gross in 1984, he regained it in 1986 with a swim of 52.84 seconds.

In 1988, on the heels of a record 11th National Collegiate Athletic Association (NCAA) individual championship at Stanford University, Morales surprisingly failed to qualify for the 1988 Olympics.

After briefly retiring from the sport to pursue a JD degree at Cornell Law School in Ithaca, New York, Morales returned to swimming and qualified for the 1992 Olympics in Barcelona, where he was the US team captain and captured gold in the 100-meter butterfly.