Environmentalists say the amusement park is responsible for contaminating the waterway.
"And what we see is really high levels of toxic metals, things like cadmium and copper and zinc," said Liz Crosson, director of the Santa Monica-based environmental group called Baykeeper.
She provided photos of the river that show debris and trash that she says came from the park.
"We have a good indication it's coming from Magic Mountain because the trash actually has their logo all over it," she said.
Baykeeper and several other environmental groups say they will sue Magic Mountain unless the theme park takes immediate action to eliminate pollution from the park ending up in the river.
"They could have more trash cans, they could have more sweeping going on, to picking up trash," she said.
A spokeswoman for the theme park denies the allegations and says the theme park has been in compliance with state regulations. In a written statement, Sue Carpenter said:
"Six Flags has been proactive in our efforts to meet the requirements of the Regional Water Quality Control Board. In light of all the due diligence that we have done, working hand in hand with this agency, the letter we received comes as a surprise. We intend to keep partnering with this board to further reduce our impact on the environment."
Clearly, not all this trash is coming from Magic Mountain, but environmentalists say the park needs to do more to be a better neighbor.
"The Santa Clara River is a very special water way in Los Angeles," said Crosson. "It's actually the last free-flowing river of that size."
But the park says it's possible that some of the pollutants the environmental groups found could be coming from upstream, not the park itself.
The environmental groups say they are giving the park 60 days to respond to their letter regarding the threat of a lawsuit.