Mr Marks told BBC Radio Cornwall water samples confirmed pollutants had “sufficiently diluted and washed away”.
While the source of the pollution had been identified and stopped, he declined to specify whether it was industrial or agricultural, citing legal sensitivities.
“I don’t want to prejudice that follow-up regulation activity, but I can reassure people that it has been stopped,” he said.
“We will be undertaking a very robust investigation.
“We will hold polluters to account where they impact the environment.”
South West Water said: “We are aware of the reports and we are supporting the Environment Agency with its investigation.”