The activists paddled into the base in canoes, evading police security boats, and managed to unfurl a large banner along the quay reading "Stop Plutonium," before 13 of them were arrested.
The incident "passed off without any injuries and only lasted a few minutes," a naval spokesman said.
All those detained were later freed.
The activists were protesting plans to unload 150 kilos of US military-grade plutonium, part of surplus stocks left over from the cold war, at the port in northwestern France.
The plutonium is due to be transported to the Cadarache nuclear re-processing facility in the southeast of the country.