The next step is to figure out where it's coming from and how it can be stopped.
Tucked away under a canopy of trees, it's tough to believe Thornton Creek is just footsteps away from busy Lake City Way.
"It's kind of a place of respite and repose," said Ruth Williams of the Thornton Creek Alliance.
While it's a hidden place, it isn't untouched -- and that's the problem.
"It looks very nice," Williams said. "You would not know the water needs so much work."
Scientists have studied the creek for decades, and the most recent investigation had some startling results.
"We found bacteria that is specific to human beings in the creek, which would've come from human fecal material," said SPU stormwater scientist Dr. Jonathan Frodge.
The human waste appears to be entering the stream in several places. Scientists made the discovery after a two-year investigation and say the levels pose a threat to public health.
"I would say yes, there is a concern," Frodge said. "We are talking about counts that are significantly higher than the criteria which are set to protect human health."
The concern is that people who might not know the creek is contaminated will bring pets or kids to play nearby.
The next step is figuring out where the fecal matter is coming from. Once scientists know the source, they hope to control or eliminate it.
"We want to bring the creek up to where it's healthy for everyone and a good habitat for all kinds of creatures," Williams said.
Seattle Public Utilities will be putting up eight additional signs along the creek warning people not to go in.
The study was the first to identify sub-basins, or general areas where bacteria appears to be entering the creek. Scientist will again study it this summer and into the fall, and in the process the hope to find the source of the contamination.
More information about the contamination is available here.