Jones was last seen at his home just outside Wharton, Texas at 10:30 p.m. on June 22, 2007. He has never been heard from again. He was reported missing the next day, after he did not show up to host his Saturday morning radio show on at KULP in El Campos, Texas. He was a locally famous musician in 2007 and played polka in the Bobby Jones Czech Band, but has not attended any gigs since his disappearance. Jones had canceled several upcoming music engagements without explanation prior to his disappearance. There was no sign of a struggle at his house.

Authorities believe Jones got in a car accident while on his way to work on June 23. They found tire tracks leading off the road to the Colorado River along Jones's work route, and when the floodwaters receded, the license plate for Jones's car was located. A search of the river turned up the car itself, a red four-door 1993 Chevrolet Lumina. Investigators have been unable to remove the vehicle from the water, however, or to search for Jones's body, because the currents are too fast and it would be dangerous.

Foul play is not suspected in Jones's disappearance. His body, which may be in the Colorado River, has not been recovered.