Dissolved Oxygen Depletion in the Stockton Deep Water Ship Channel: Conceptual Models

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Home Site Map About These Models Definition of a Conceptual Model Subject of these Conceptual Models Purpose of these Conceptual Models Structure of these Conceptual Models Geographic Scope Navigation Tools Links to Other Models Sources of Information Authors and Acknowledgments Comment or Contribute Tools Terminology Acronyms References-Biological Model References-Physical Model Biological and Ecological Effects Model Physical and Chemical Processes Model

About These Conceptual Models

Definition of a Conceptual Model

A conceptual model describes the current state of scientific understanding of a subject. The purpose of a conceptual model is to provide enough information on each model component to allow the subject to be understood at a conceptual level. A conceptual model is not intended to be a mathematical model or to provide comprehensive information on every component.

Subject of These Conceptual Models

San Joaquin River at MossdaleThe subject of these conceptual models is DO concentrations in the Stockton DWSC on the San Joaquin River of California. To address this complex subject, two conceptual models have been developed:

In addition, the models describe how important each driver is in influencing either DO concentrations or the effects of low DO concentrations on the ecosystem and how well understood the mechanisms behind each driver are.

The text associated with these models is not comprehensive. Instead, it provides a detailed but not exhaustive description of the science and includes links to the source documents for the reader who wants to explore a subject further.

In addition, the models are meant to be living documents. Much work is being done in studying the causes and effects of low DO concentrations, and it is the intent that the models will be modified as new data or studies become available.

Purpose of These Conceptual Models

The Physical and Chemical Processes Conceptual Model and the Biological and Ecological Effects Conceptual Model were developed for two main purposes.

First, the models are intended to provide a comprehensive overview of the current state of scientific understanding of the drivers that affect DO concentrations in the DWSC and the biological and ecological effects of low DO concentrations. The models focus on the DWSC because DO concentrations frequently drop below the standards in The Water Quality Control Plan for the Sacramento River and San Joaquin River Basins (Basin Plan) (CVRWQCB 2004) adopted by the Central Valley Regional Water Quality Control Board. Further, numerous resource management documents identify low DO concentrations in the DWSC as an area of concern.

Second, the models are intended to identify those drivers that are not well understood but are thought to have the largest effects on outcomes (i.e., DO concentrations in the physical/chemical model or on fish in the biological/ecological model). New studies or data collection efforts focused on these drivers would be expected to improve our understanding of the problem.

Model Structure (Driver-Linkage-Outcome Format)

As described above, the factors influencing DO concentration in the DWSC and its effects are described using two conceptual models, a physical/chemical model and a biological/ecological model. Each model is structured using the driver-linkage-outcome format favored by the California Bay-Delta Authority.


Outcomes are the environmental or physical conditions that are the target of management actions. In the physical/chemical model, the primary outcome is the concentration of DO in the DWSC. In the biological/ecological model, the primary outcome is effects on fish species.


Linkages are the known or hypothesized mechanisms by which the drivers influence the outcomes. For example, in the physical/chemical conceptual model for DO in the DWSC, CBOD is a primary driver. The linkage that connects CBOD concentrations with DO concentrations is the biochemical pathways that break down CBOD and consume oxygen, decreasing DO levels. Linkages also have attributes associated with them, including direction (i.e., increase or decrease), importance, and certainty.


Drivers are factors thought to influence outcomes. Because of the complexity of the physical/chemical and biological/ecological conditions in the San Joaquin River, both conceptual models consist of both primary and secondary drivers. As an example, one of the primary drivers for DO is BOD. In turn, a variety of secondary drivers determine the levels of BOD in the aquatic environment (e.g., algal biomass, nonalgal organic matter, residence time, water temperature).

The designation of drivers as primary or secondary drivers does not imply relative importance of these drivers in influencing DO concentrations. Rather, the drivers are organized by cause and effect relationships, so that the primary drivers directly affect the DO concentrations and the secondary drivers indirectly affect DO concentrations by influencing the primary drivers. In fact, some secondary drivers, such as channel geometry, flow, and algal biomass, are thought to be among the more important factors influencing DO concentrations in the DWSC.

Geographic Scope of the Conceptual Models

These conceptual models encompass the San Joaquin River from Friant Dam to the central Delta. For the purposes of this model, the river has been divided into three reaches (see below). The Physical and Chemical Processes Conceptual Model evaluates this entire stretch of the San Joaquin River. The Biological and Ecological Effects Conceptual Model focuses mainly on the reach comprising the DWSC because this is the area subject to low DO episodes.

Overview map of the San Joaquin River

Reach 1

Reach 1 comprises the river from Friant Dam to Vernalis. Friant Dam was selected as the upstream terminus because few, if any, inputs of oxygen-demanding substances or their precursors occur upstream of Friant Dam. Although Friant Dam was selected as the upstream boundary of the physical/chemical conceptual model, San Joaquin River flows are very limited between Friant Dam and the downstream confluence with Bear Creek because of channel infiltration losses and diversions.

Vernalis was chosen as the downstream terminus for two main reasons. First, it represents the downstream edge of the river unaffected by tidal influences. Second, it is a compliance location for water quality regulations, so a great deal of water quality data is available.

Reach 2

Reach 2 comprises the river from Vernalis to Channel Point. This reach encompasses the portion of the San Joaquin River that transitions from river to estuary. Channel Point was chosen as the downstream terminus because it is where the river enters the DWSC.

Reach 3

Reach 3 is the DWSC, which extends from Channel Point to Disappointment Slough. This reach also includes the last mile of the dredged DWSC, which is not part of the San Joaquin River, from Channel Point to the Turning Basin. Although the DWSC actually extends through the Delta and into San Francisco Bay, Disappointment Slough was selected as the downstream terminus because flows of water across the Delta from the Sacramento River dominate the water quality at this point, so it represents the downstream edge of the area of DO impairment. Low DO concentrations are typically not seen downstream of Disappointment Slough.

Navigation Tools

example of horizontal navigationIn a paper-based conceptual model, the organization of the information is fixed and linear. Because these two conceptual models are web based, the reader has the option of looking at the information contained in them in a variety of ways.

For example, in the biological/ecological model, the information is organized by primary driver, then secondary driver, then fish species. In addition, links are provided in the text that enable the reader to move “sideways” in the model (i.e., by secondary driver or species) (see screenshot at right). Thus, a reader interested in information on a particular species can easily navigate sideways to all the text for that species.

Links to Other Models

When other web-based conceptual models are available, links will be provided to these models.

Sources of Information

The information contained in these conceptual models has been synthesized from dozens of sources. Citations for the source documents or data are included in the text. Clicking on a citation (in blue) will take you to the full reference for the cited document. In addition, most of the references provide a link (also in blue) that will connect the user to an electronic copy of the document.

Authors and Acknowledgments

These models were developed under the guidance and with the support of the California Bay-Delta Authority, Ecosystem Restoration Program (ERP).

  • Rhonda Reed, California Bay-Delta Authority—ERP Program Manager
  • Barbara Marcotte, California Bay-Delta Authority—ERP Project Manager
  • Mark Gowdy, Central Valley Regional Water Quality Control Board—Regional Board Project Manager
  • Craig Stevens, Stevens Consulting—Consultant Project Manager
  • Tim Messick—Graphics and Website Programming
  • Ellen Unsworth—Lead Editor
  • Darle Tilly—Editor
  • Sharon Hoepker—Librarian

Technical Contributors for the Physical and Chemical Processes Model—Jones & Stokes

  • Russ Brown, PhD.
  • Pete Rawlings
  • Lea Adams, P.E.
  • Megan Robinson

The Physical and Chemical Processes Model was created using a variety of information sources. The document Synthesis and Discussion of Findings on the Causes and Factors Influencing Low DO in the San Joaquin River Deep Water Ship Channel near Stockton, CA: Including 2002 Data (Lee and Jones-Lee 2003), which summarized historical data and discussed several research projects funded by CALFED in 2000 and 2001, was a major source of information for this model. Many other sources of information were also used to develop the conceptual model.

Technical Contributors for the Biological and Ecological Effects Model—Jones & Stokes

  • William T. Mitchell
  • Jonathan Rosenfield, PhD.
  • Martin Koenig