TMDL Projects
San Joaquin River Dissolved Oxygen TMDL
Required Studies

To request a copy of documents listed on this page, please contact Jennifer LaBay at Jennifer.LaBay@waterboards.ca.gov or (916) 464-4650.

The TMDL required the completion of specific oxygen demand and precursor studies. These source and linkage studies were to identify and quantify:

  1. Sources of oxygen demanding substances and their precursors in the dissolved oxygen TMDL source area
  2. Growth or degradation mechanisms of these oxygen demanding substances in transit through the source area to the DWSC
  3. The impact of these oxygen demanding substances on dissolved oxygen concentrations in the DWSC under a range of environmental conditions and consider the effects of chemical, biological, and physical mechanisms that add or remove dissolved oxygen from the water column in the DWSC.

The studies were broken down into two different study efforts. The first set of studies, referred to as the "Upstream Studies", mainly focused on the riverine reach of the San Joaquin River between Highway 165 at Lander Avenue to Vernalis with additional research conducted further downstream from Vernalis to Channel Point. The second set of studies, referred to as the "Downstream Studies", mainly focused on the estuarine reach of the San Joaquin River between Mossdale to Turner Cut with additional research conducted at main stem monitoring sites located upstream of Vernalis.

An Independent Peer Review was conducted on the modeling tools developed as part of the TMDL studies. The final reports for the Upstream and Downstream Studies as well as the Peer Review Report can be found below.

Source and Linkage Studies

  • San Joaquin River Upstream DO TMDL Project - "Upstream Studies"

    These studies were undertaken in the "Monitoring and Investigations of the San Joaquin River and Tributaries Related to Dissolved Oxygen" and were conducted from June 2005 through December 2007. The final report was completed in June 2008 and included numerous task reports and associated appendices.
    • Task 12 - DO Project Final Report:
      • Up-Stream DO TMDL Final Report
    • Task 4 - Monitoring in the Up-Stream Source Area:
      • Monitoring Study
      • Appendices A-V (including data)
    • Task 5 - Upgrade of Monitoring Stations:
      • Description of Flow and Water Quality Monitoring Upgrades and Photo Documentation
    • Task 6 - Modeling Study:
      • Final Report for the Task 6 Modeling of the San Joaquin River
    • Task 7 - BOD Isotope Study:
      • Linking the San Joaquin River to the Stockton Deep Water Ship Channel
    • Task 8 - Linking Study:
      • Final Report for the Task 6 Modeling of the San Joaquin River
    • Task 9 - Grazing Study:
      • An Analysis of Grazing and Phytoplankton Communities in the Lower San Joaquin River Above the Stockton Deep Water Ship Channel
    • Task 10 - New Station in Tidal Estuary:
      • Installation of a New Monitoring Station for the San Joaquin River
    • Task 11 - Data Storage:
      • Local Access Database

  • Independent Peer Review and Panel Report:

    In September 2013, the California Department of Fish and Wildlife Ecosystem Restoration Program provided funding for an Independent Peer Review of the models developed as part of the Control Program studies. The Charge to the Panel and the Panel Report are included below.
    • Charge to the Panel
    • Kratzer, C., Deas, M., Fleenor, B., Paerl, H. 2013. Review Panel Report: The San Joaquin River Stockton Deep Water Ship Channel Dissolved Oxygen Total Maximum Daily Load - WARMF and Link-Node Models

  • San Joaquin River Downstream Estuary DO TMDL Project - "Downstream Studies":

    These studies titled, "Characterizing the Impact of Upstream San Joaquin River Algae Loads on Dissolved Oxygen Conditions in the Stockton Deep Water Ship Channel" were approved in August 2008 The studies were not immediately started because of lack of funding and are waiting for funding. In 2012, grant funding was provided by the California Department of Fish and Wildlife Ecosystem Restoration Program and the Estuary Project was initiated. The project completed in December 2013, and the final report and associated task reports were submitted in September 2014.
    • Task 7 - Final Reports:
      • 7.1.1 Synthesis of Results from Investigation of the Causes of Low Dissolved Oxygen in the San Joaquin River & Estuary in the Context of the Dissolved Oxygen Total Maximum Daily Load
      • 7.2.1 San Joaquin River Dissolved Oxygen Total Maximum Daily Load Program Long term Monitoring Plan
    • Task 4 - Data collection and Data Distribution:
      • Subtask 4.1 - Water Quality and Flow Data from the Upstream SJR Study Area
        • 4.1.1 Description and Photo-Documentation of Field Work Activities - Westside Monitoring Station Maintenance
        • 4.1.2 Summary of Analytical Methods, Quality Assurance, and Quality Control for 2011 and 2012 Field Sampling and Laboratory Water Quality Analysis
      • Subtask 4.2 - Collection of Water Quality, Flow, and Other Data from SJR Estuary Study Area
        • 4.2.1 Description and Photo-Documentation of Field Work Activities
        • 4.2.2 Summary of 2011 and 2012 Field and Laboratory Water Quality Data
        • 4.2.3 Temporal Plots of Field and Laboratory Data for Each Site Sampled in 2011 and 2012
      • Subtask 4.3 - Survey Water Quality in the Old and Middle Rivers
        • 4.3.1 Dissolved Oxygen Conditions in the Old and Middle Rivers in 2011 and 2012
      • Subtask 4.4 - Zooplankton Distribution in the SJR Estuary
        • 4.4.1 Spatial Heterogeneity of Zooplankton in the Stockton Deep Water Ship Channel
        • 4.4.2 Zooplankton Grazing Studies
      • Subtask 4.5 - Microcystis and Blue-Green Algae in the SJR Estuary
        • 4.5.1 Unprecedented Bloom of Toxin-Producing Cyanobacteria in the Southern Bay-Delta Estuary and its Potential Negative Impact on the Aquatic Food-Web
      • Subtask 4.8 - Data Analysis and Interpretation
        • 4.8.1 Using the WARMF 2008 Model to Quantitate the Effect of Nutrient Control and Tributary Inputs on Water Quality in the San Joaquin River
        • 4.8.2 Analysis of the Gowdy Output Results from the SJR-WARMF 2012 Model
        • 4.8.3 Mass Balance Analysis for the San Joaquin River from Lander Avenue to Vernalis
        • 4.8.4 Methods for Direct Load Calculations in Agricultural Watersheds
        • 4.8.5 Analysis of Link-Node Model Mass Loading Scenarios
        • 4.8.6 High Resolution Dissolved Oxygen Profiling of the Stockton Deep Water Ship Channel during the Summer of 2012
        • 4.8.7 High Resolution Salinity Profiling of the Stockton Deep Water Ship Channel during the Summer of 2012
        • 4.8.8 SJR-WARMF 2008 and 2012 Error Analysis
    • Task 5 - Modeling:
      • Subtask 5.1 - Maintenance and Support of San Joaquin River Model Interface
        • 5.1.1 Calibration of the Link-Node Model for Application to Understanding Causes of Low Dissolved Oxygen Conditions in the Stockton Deep Water Ship Channel
      • Subtask 5.2 - Focused Agricultural Drainage Study
        • 5.2.1 San Joaquin River Water Quality Modeling: Suspended Sediment Modeling of San Joaquin River in Watershed Analysis Risk Management Framework (WARMF) Model
        • 5.2.2 Orestimba Creek Agricultural Drainage Study
        • 5.2.3 Focused Agricultural Drainage Study: Calibration of the Orestimba Creek Watershed in the San Joaquin River WARMF Model
      • Subtask 5.6 - Simulation of Zooplankton Dynamics in the Link-Node Model
        • 5.6.1 Inclusion of Zooplankton Population Dynamics in the Link-Node Model
    • Task 6 - Meeting Presentations:
      • 6.1.1 Presentations and Abstracts for the Dissolved Oxygen Total Maximum Daily Load Project
    • Task - Data Collection:
      • Data collection includes: water quality grab sample data, water quality survey data, and continuous water quality data from the Westside.