In 1998, the Oregon Department of Environmental Quality (DEQ) added Johnson Creek to the list of waterbodies on its 303(d) list. A waterbody that is water quality limited for certain parameters is placed on this list under section 303(d) of the federal Clean Water Act.

Johnson Creek is listed as water quality limited for bacteria, summer temperature, and toxics (DDT and dieldrin). In 2002, the DEQ added PCBs (polychlorinated biphenyls) and PAHs (polycyclic aromatic hydrocarbons) to the 303(d) for Johnson Creek. The listing includes the entire stream from the mouth to the headwaters.

After a waterbody is placed on the 303(d) list, the next step is developing total maximum daily loads (TMDLs) for the listed parameters. The DEQ started the TMDL process for Johnson Creek in 2001, developed TMDLs for temperature, bacteria, DDT, and dieldrin and issued these TMDLs as part of the Willamette Basin TMDL approved by the U.S. Environmental Protection Agency (EPA) in September 2006.

The DEQ will develop TMDLs for PCBs and PAHs at a later point. The city has been implementing the TMDL requirements for a number of years and is making progress toward meeting the load allocations set by the TMDL process.