In 1998, there were only two stream/river reaches within the Clackamas watershed listed as water quality limited on the state’s 303(d) list.  The Lower Clackamas from its mouth to the Mill River Dam, was listed for increased temperatures too extreme for salmonid spawning and rearing. Fish Creek, a major Clackamas tributary, was formerly listed for temperature, and is currently still limited due to Habitat Modification. This parameter refers to stream habitat particularly as it applies to fish- including pools, riffles, or woody debris. Late run winter coho and native winter steelhead are on the decline partially due to the absence of adequate large woody debris and pool habitat. 

For the 2002 water quality limited list (303(d) list), several lower Clackamas tributaries were added for bacterial contamination.  Countless other reaches within the Clackamas watershed are considered by the state to be of potential concern for parameters such as concentration of toxics, bacteria, pH, sedimentation, DO, flow modification, nutrients and Chlorophyll a. Data needs to be collected and analyzed for these reaches.