The EC145 rescue helicopter lost radio and radar contact with controllers as it headed to Le Luc - Le Carnet in the hilly Var region.
The bodies of the three occupants were found at about 1.30am, an interior ministry statement said.
France's Mediterranean coast has been hit by heavy rain over the last week that has led to serious flooding and widespread transport disruption.
Interior Minister Christophe Castaner drew a parallel between the three workers to 13 French soldiers who were killed last week in Mali while fighting Islamist militants and who were being honoured on Monday in Paris.
"As France prepares today to mourn 13 of its soldiers who died serving the nation, our country is losing three everyday heroes who gave their lives to protect the people of France," Castaner and his deputy said in a statement.
Local officials reported the deaths of two people swept away by the floodwaters.
French media reported that one was a shepherd whose 4x4 vehicle was carried away by a flashflood as he crossed a ford. The other was the owner of a stable who had been out watching over his animals.
