Monitoring Special Study

On December 12, 2018, the State Water Resources Control Board (Water Board) amended the Water Quality Control Plan (Resolution No. 2018-0059) for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (Bay-Delta Plan). The amendments include revised salinity objectives for the southern Delta and instruct the California Department of Water Resources (DWR) and United States Bureau of Reclamation (Reclamation) to develop a Monitoring Special Study (MSS).

Since early 2021, DWR and Reclamation have been soliciting input from participating agencies and working with Water Board staff to design four technical studies as part of the MSS.

On September 19, 2022, consistent with Section B(1)(iv) of the Program of Implementation for the Bay-Delta Plan, DWR and Reclamation submitted to the Water Board its Monitoring Special Study Plan for the 2018 Bay-Delta Plan (MSS Plan), designed to accomplish the following goals:

Characterize the spatial and temporal distribution and associated dynamics of water level, flow, and salinity conditions in the southern Delta waterways.
Identify the extent of low or null flow conditions and any associated concentration of local salt discharges.
Inform the development of a Long-Term Monitoring and Reporting Plan that will:

Assess attainment of the salinity objective in the interior southern Delta.
Include long-term monitoring and reporting protocols, including specific compliance monitoring locations in, or monitoring protocols for, the three river segments that comprise the interior southern delta salinity compliance locations.

The MSS Plan, linked in the ‘Documents’ section below, further specifies these goals, approaches to meeting them, a map showing the geographic scope of the MSS, and descriptions of the four technical studies. Descriptions of the four technical studies are also provided below. Detailed information of each technical study is available in its corresponding work plan, found in Attachments 1 – 4 in the Documents section.

Development of the MSS Plan has involved continuous outreach and feedback from participating organizations. Appendices A and B of the MSS Plan capture some of the feedback and engagement received from participating organizations leading up to the September 2022 MSS Plan submittal. The MSS Plan was conditionally approved by the Water Board on May 5, 2023.

Future public meetings are planned to continue through the duration of the MSS to share updates and solicit feedback on preliminary findings. For more information on future public meetings and to be added to the participating organization contact list, please contact Bill McLaughlin at William.McLaughlin@water.ca.gov.

Dye Tracer Study conducted at Paradise Cut on July 19, 2022 using rhodamine dye to measure mean transport and dispersion rates of water in upper Paradise Cut with the goal of understanding high salinity water exchange and downstream transport into Old River.

Technical Studies

High Speed Salinity Transect Mapping Study

DWR monitors Electrical Conductivity (EC) values from several water quality monitoring stations throughout the southern Delta, as required by the Water Board in Decision 1641. These monitoring stations provide EC values at a stationary location and do not provide information on variation of water quality between stations. This study attempts to get a better understanding of EC levels over specific channel reaches by utilizing a vessel equipped to capture EC values and associated position data. The changes in EC over space and time will be rapidly measured and processed into maps to provide visualizations of the longitudinal salinity transects to see where low or null flow conditions are allowing salinity to concentrate.

Salinity Point Source Sampling and Ion Sampling Study

This study is a comprehensive data collection effort that involves installing temporary EC monitoring stations in targeted areas to improve modeling resolution and increase confidence in modeling results. Ion samples will also be collected and analyzed to develop ionic fingerprints that could distinguish between salinity sources. Additional monitoring efforts will be conducted as needed, including dye tracing experiments that will provide models with improved dispersion rates and confirm mean flow direction in channels with low flow magnitude, such as Paradise Cut.

SCHISM 3D Hydrodynamic and Water Quality Modeling Study

The Semi-Implicit Cross-scale Hydroscience Integrated System Model (SCHISM) component of the MSS is intended to provide a means of synthesizing observations from enhanced monitoring, examining hypotheses, and applying insights to developing monitoring protocols for the three interior southern Delta River segments. The model will be used to define and assess different approaches to compliance across the three river segments and can be used to assess the likelihood of compliance under different flow regimes. Simulations will also be performed to assess the relative influence of Vernalis inflow, Vernalis water quality, State and Federal Project exports, and in-Delta sources. Early stages of this study will require refining the mesh for the interior southern Delta to achieve better resolution of small bathymetric and flow features. A finer mesh will also inform data collection and analysis and identify knowledge gaps concerning the spatial and temporal distribution of null flow zones.

Water Quality Data Assimilation Study

Data assimilation is a modeling technique that is used to infer unknown salinity sources to integrate observational data with a mechanistic model to provide additional insight on EC sources and identify data gaps required to better monitor the system. The inferred salinity loads as a data product can be used to improve model performance of EC outputs for both DSM2-GTM (General Transport Model) and SCHISM. This model utilizes data that are quality assured and controlled from an extensive continuous monitoring network, hosted on DWR’s Water Data Library and the United States Geological Survey’s National Water Information System, along with additional data collected from the monitoring components of the MSS, and integrates the data with a mechanistic water quality model. This approach can provide insight to the underlying causes of the high level of salinity observed in the southern Delta. Additionally, with hydrodynamic and salinity transport models, Data Assimilation can provide more realistic modeling of the spatial and temporal distribution of water level, flow, and salinity conditions in the southern Delta system.

Document List

Public Coordination Meetings

Public Coordination Meeting #1: May 6, 2021
- Notes
- Slides
Public Coordination Meeting #2: October 12, 2021
- Notes/Slides
- Link to Mural Page
Public Coordination Meeting #3: May 17, 2022
- Notes
- Slides
Public Coordination Meeting #4: March 20, 2023
- Notes
- Slides
Public Coordination Meeting #5: October 3, 2023
- Notes
- Slides
Public Coordination Meeting #6: March 15, 2024
- Notes
- Slides

Technical Workgroup Meetings

Technical Workgroup #1: June 14, 2021, Paradise Cut Flushing
- Notes
- Handout
Technical Workgroup #2: July 13, 2021, Water Quality Data Integration (Data Assimilation)
- Notes
- Slides
Technical Workgroup #3: July 19, 2021, Salinity Point Source and Ion Sampling
- Notes
- Slides
Technical Workgroup #4: January 13, 2022, SCHISM & Related Modeling
- Notes
- Slides
Technical Workgroup #5: March 17, 2022, Discussion of the 1980 Report
- Notes
- Slides
Technical Workgroup #6: September 15, 2022, High Speed Salinity Transect Mapping
- Notes
- Slides
Technical Workgroup #7: December 9, 2022, SCHISM and Data Assimilation
- Notes
- Slides
Technical Workgroup #8: June 30, 2023, MSS Modeling Assumptions Response to Comments
- Notes
- Slides
Technical Workgroup #9: December 12, 2023, MSS Data Assimilation: an Introduction
- Notes
- Slides

Monitoring Special Study

Technical Studies

High Speed Salinity Transect Mapping Study

Salinity Point Source Sampling and Ion Sampling Study

SCHISM 3D Hydrodynamic and Water Quality Modeling Study

Water Quality Data Assimilation Study

Document List

Public Coordination Meetings

Technical Workgroup Meetings

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