Dissolved Oxygen Depletion in the Stockton Deep Water Ship Channel: Physical and Chemical Processes Conceptual Model

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Reach 3 (Channel Point to Disappointment Slough)

Click on a primary driver to see the secondary drivers that influence it and to read reach-specific discussions of those drivers.

To view information for other reaches, click on the appropriate reach in the map.

General (non–reach specific) information about each primary driver and the secondary drivers that influence it is provided in the Basic Concepts section. This information includes definitions, general scientific principles, and interactions among drivers.

Reach 3 map
Reach 3 diagram

Dissolved Oxygen Concentrations in the
Stockton Deep Water Ship Channel

The ultimate outcome of the Physical and Chemical Processes Conceptual Model is the DO concentration in the DWSC. As described below, the CVRWQCB and the California Bay-Delta Authority are working to improve DO concentrations in the DWSC. This section answers the following questions about DO in the DWSC:

What Are the Dissolved Oxygen Concentrations in the Stockton Deep Water Ship Channel?

Data on DO concentrations in the DWSC have been collected since 1984. These data have been summarized in graphic form for the Biological and Ecological Effects model. The full data set is included in the San Joaquin River Water Quality Data Atlas, portions of which are available for download (see "DWSC DO 1984–2005" on the Data Atlas page).

The graphic below shows that low-DO episodes have occurred every month of the year but are most common in the summer and fall (June–November). DO concentrations frequently fall below the regulatory minimum set in the Basin Plan and even fall below 2 mg/L.

As described in this model, DO concentrations in the DWSC are affected by drivers in Reach 1 and Reach 2, as well as drivers in the DWSC itself. As described below an in the Biological and Ecological Effects Model, DO concentrations are important because of their effect on beneficial uses, including effects on fish.

DO and Temperature by Month in the Study Area

Dissolved Oxygen and Oxygen-Demanding Substances Contributed from Reach 3 to Downstream

Sources, timing, and magnitude of DO and the contribution of substances from Reach 3 that can generate oxygen demand downstream (e.g., algal nutrients) are not well understood. Concentrations of oxygen-demanding substances have been measured at City of Stockton monitoring stations R8 (between Disappointment Slough and Turner Cut) and R7 (between Turner Cut and Fourteen Mile Slough). At monitoring station R7, TSS and VSS concentrations were 20–30% less than the concentrations measured at the R3 station (Jones & Stokes 2002a) near Channel Point. In addition, BOD5 and VSS concentrations at the R8 station were generally lower than concentrations upstream (Jones & Stokes 2002a; Jones & Stokes 2001a).

In June 2001, the BOD5 and VSS concentrations at R8 were 1–2 mg/L and 3 mg/L, respectively (Jones & Stokes 2002a). The DO depletion in Reach 3 can be described as a DO sag pattern, with the DO concentrations generally declining from Channel Point to a location downstream of the Rough and Ready Island monitoring station, and then slowly increasing toward Turner Cut. A greater fraction of the BOD loads move downstream with higher flows (i.e., lower residence time). During lower flows, more of the BOD in Reach 3 is exerted in Reach 3 and less is transported downstream.

DO concentrations in water leaving Reach 3 are generally greater than DO concentrations further upstream in the DWSC (Hayes & Lee 2000a). Generally, DO concentrations near Disappointment Slough are greater than the regulatory minimum of 5 mg/L or 6 mg/L (Hayes & Lee 2000a) and are relatively stable (Hayes and Lee 2000b). Transport of higher quality Sacramento River water across the Delta toward Turner Cut is likely one factor responsible for the higher DO concentrations (Jones & Stokes 2001a) at the downstream end of Reach 3.

Why Are Dissolved Oxygen Concentrations in the Stockton Deep Water Ship Channel Important?

The San Joaquin River experiences regular periods of low DO concentrations in the first few miles of the Stockton DWSC downstream from the City of Stockton. These conditions often violate the water quality objectives for DO in the DWSC as contained in the Basin Plan. The Basin Plan specifies that DO levels in the San Joaquin River between Turner Cut and Stockton should not fall below 5 mg/L December through August and 6 mg/L September 1 through the end of November.

In January 1998, the State Water Resources Control Board first adopted a Clean Water Act Section 303(d) list that identified this impairment and ranked it as a high priority for correction.

Inclusion on this list initiated the need, under the Clean Water Act, for the CVRWQCB to develop a TMDL that identifies the factors contributing to the DO impairment and apportions responsibility for correcting the problem. It also initiated the need, under the Porter-Cologne Water Quality Control Act, to develop a program of implementation for the TMDL consisting of actions that the regional board would take to implement this TMDL and to bring the impaired reach of the DWSC into compliance with the Basin Plan DO objectives (Gowdy and Grober 2005).

In addition, resource management documents have identified low DO conditions in the DWSC as a possible stressor on resident and anadromous fish in the Delta. These conditions are thought to block the downstream migration of juvenile salmonids and to lead to other adverse effects on fish. The Biological and Ecological Effects Model describes the conditions that lead to adverse effects on fish and describes in detail what is known about how low DO conditions affect eight fish species.

The involvement of the California Bay-Delta Authority is based on the CALFED 2000 Programmatic Record of Decision, which contains a commitment to address low-DO conditions in the DWSC. The preferred program alternative under the Water Quality Program states "Low dissolved oxygen – Reduce the impairment of rivers and the estuary from substances that exert excessive demand on dissolved oxygen." Since 1999, stakeholders and other agencies have been working with the Central Valley Regional Water Quality Control Board and California Bay-Delta Authority to develop and implement a TMDL. This conceptual model was developed to assist in that effort.

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