The employees made the macabre discovery in a stretch of the river in Döttingen at 9am, police said.
An investigation is under way to determine whether it the two-year-old boy Cyrill, reported missing in Windisch on April 25th.
The child's father told officers that the boy vanished from his sight while they were on an evening outing on the banks of the Reuss River, according to earlier police information.
An initial search failed to find the boy.
Investigators later searched the man's apartment, according to media reports.
And the local prosecutor's office announced that an investigation was under way for putting a life at danger and negligence.
“We are conscious of the tragic situation of this man but we must do our work,” prosecutor Fiona Strevel earlier told 20 Minuten newspaper.
The disappearance of Cyrill came a week after another two-year-old boy Semere was reported missing after playing near the Chur River in the canton of Saint Gallen.
The boy had wandered away from his Eritrean parents while they were attending a baptism ceremony in a church in Wattwil.
His body was found in the Chur River on May 6th, with his identity later confirmed by forensic scientists, Saint Gallen cantonal police said.
Elsewhere on Thursday, hikers discovered a body tangled in branches in the river bed of the Doubs in the canton of Jura.
Cantonal police said it was found near Saint Ursanne.
A process is under way to identify the body, police said.
In mid-March a woman living in a home for seniors in Saint Ursanne was reported missing and a search for her has been ongoing.