The Deschutes River is the largest drainage in WRIA 13, providing over 256 linear miles of drainage before emptying into Budd Inlet through Capitol Lake. Primarily one commercial timber company owns the upper watershed of the river and its tributaries.

Urbanization has heavily impacted the lower reaches of the river. Capitol Lake was created as a reservoir at the mouth through damming the lower Budd Inlet estuary in the 1950's. A Chinook hatchery program includes adult capture, along with rearing pens above a fish ladder at the natural falls in Tumwater and in Percival Cove in Capitol Lake. This program releases 3.8 million sub-yearling and 200,000 yearling Chinook each year[1]. A new comprehensive Chinook hatchery complex is in conceptual design, which would add incubation and new rearing facilities. No natural anadromous fish passage exists past this point just above the mouth, although fish managers have introduced Chinook and coho above the falls since the 1950's.

The presence of Capitol Lake and the continued operation of the tide gate prohibit the system's ability to function naturally. During the winter months, the tide gate operation impedes juvenile access as lake levels are below what is necessary to allow access to the fish ladder. Out-migrating smolts must transition from fresh to salt water immediately due to the presence of the tide gate that prevents naturally occurring mixing that happens in a natural estuary. Sediment accumulation in the lake creates shallow areas that have increased water temperature. Additionally, attempts to manage the lake level for storm events have left the rearing area dry in some cases or lead to an early release of smolts in others. Currently, the State of Washington General Administration is heading an effort to study the management of Capitol Lake, evaluating the options of continuing to maintain the lake as a reservoir or to return it to an estuary.

Human efforts to limit erosion upstream from the falls has inhibited channel migration, thereby limiting off-channel areas for rearing in the lower reaches at the mouth. In the middle and upper reaches however, wetlands and off-channel areas exist in several locations. Much of the middle and upper reaches of the basin are rated as having fair to poor riparian conditions. A riparian assessment, currently underway by the Thurston Conservation District, will identify specific locations of degraded riparian areas so revegetation efforts can be implemented where needed.

Managed forestlands in the upper watershed and tributaries introduce fine sediment to the system; several significant forest road failures in recent years during abnormally high precipitation events accentuated this problem.

Description from the Salmon Habitat Protection and Restoration Plan for Water Resource Inventory Area 13, Deschutes. For more information see the previously stated document or the Salmon Habitat Limiting Factors Final Report Water Resource Inventory Area 13