The upper Cedar River is about 25 mi (40 km) long and can be separated into sections between Landsburg Dam and Cedar Falls (accessible to anadromous fish) and between Chester Morse Reservoir and the headwaters (inaccessible to anadromous fish). The watershed drains an area of 125 mi2 (324 km2) and is almost completely owned by the City of Seattle. The watershed is operated to provide a clean source of drinking water for Seattle and surrounding areas. As such, it is mostly forested with coniferous trees in mutli-seral stages, from old growth to recently harvested areas (logging has been discontinued in the watershed in 1993). The upper Cedar River (between Landsburg Dam and Cedar Falls) became accessible to salmon in the fall of 2003 when a fish ladder was completed at Landsburg Dam. For the entire 2003 season, a total of 79 Chinook were passed above Landsburg Dam and spawning surveys confirmed the presence of 15 Chinook redds.

With passage at the ladder, there is about 14 mi (23 km) of additional habitat now available to Chinook, characterized primarily by a narrow valley with step-pool and plane-bed channel forms. There are several tributaries that enter the river, with upper Rock Creek being the largest. The mainstem channel does not contain much woody debris, due to past practices of removing wood to protect the dam at Landsburg. However the habitat is otherwise of high quality due to the cessation of logging and lack of development. This area is used by Chinook salmon for spawning and limited rearing as they move downstream. The area of the Cedar River above Chester Morse Reservoir is the only area in WRIA 8 known to contain bull trout and bull trout use the lake for general residence and tributary areas (i.e., Cedar and Rex rivers) for spawning and rearing.

Operation of the City of Seattle's water supply facilities on the Cedar River captures 43% of the upper Cedar River watershed runoff and significantly influences stream flows and aquatic habitat throughout the river below Masonry Dam (RM 35.6). A number of activities have been implemented in an effort to avoid flow-related impacts in the river including a comprehensive Instream Flow Incremental Methodology Study (IFIM; Cascade Environmental Services, Inc. 1991), adoption of an instream flow management regime (based on the IFIM study and additional biological and hydrologic investigations), and activities implemented as part of theCedar River Habitat Conservation Plan instream flow management program (see City of Seattle 2000 [Sections 4.4, 4.5.2 and 4.6], 2002, 2003 and 2004 for more information). Instream flow management of the Cedar River aims to provide beneficial instream habitat conditions and avoid harm to fish species through a guaranteed flow regime, minimum and supplemental flow commitments, limits on stream rate reductions, and instream flow monitoring and research to inform real-time stream flow management activities. The program also includes evaluating the effectiveness of the instream flow program at avoiding impacts to fish species in the Cedar
River.