Commissioners in Brussels will discuss the inquiry on 27 November and could launch an infringement procedure if they suspect the project does not follow European regulations.
Environmentalists and local officials have been calling on the Commission for years to review whether the project fails to respect laws on the preservation of wetlands and the status of waterways.
"Since 2011, Green MEPs and people of Sivens have been asking for the Commission to say [...] the rules were not correctly adapted," French Green MEP José Bové told RFI.
Supporters of the project say the inquiry is a political move that ignores the benefits the dam would bring to farmers.
"It's an attempt of the opponents to get media attention," said Philippe Jougla of the Tarn region farmer's union, which supports the project.
The project in the Tarn department of south-west France became a source of nationwide tension following the death of 21-year-old Rémi Fraisse during a heated confrontation with police on 26 October.
Construction on the dam was suspended and the government opened an investigation into the conditions surrounding the incident.
If the Commission begins an infringement procedure, French officials would have two months to review the case, which could then be brought before the European Court of Justice.
An infraction procedure would also block European funding for the project, currently set at 2 million euros of the complete 8.4 million euro budget.
Bové hopes the review gets the French government to rethink the project.
"I hope this is going to be enough to say to the government they have to stop this project and find new answers to help the farmers," he said.