Bowden was the subject of an FBI probe into the alleged skimming of monies given to prospects from the Dominican Republic, where Rijo runs baseball academy for young players.
The Washington Post reported Gonzalez' real identity was 23-year-old Carlos Alvarez David Lugo.
When Lugo received a $1.4 million signing bonus in 2006, he was 19.
Rijo reportedly is linked to Lugo, but Nationals president Stan Kasten said Rijo's dismissal was not because of his involvement in the matter.
The Nationals will no longer use Rijo's academy, and have released 14 minor league players.
"We have replaced virtually all the staff, which includes office staff, coaches and player development people," Kasten said on the team's Web site. "We have physically removed everything from the Rijo complex and moved it to our new home."
The new home was not disclosed, but spring training is held in Viera, Fla.