Department of Water Resources Home

Water Quality Evaluation Section

North Central Region Office

Water Quality Evaluation Section


3500 Industrial Blvd.
West Sacramento, CA 95691
(916) 376-9600

Mailing Address:
P.O. Box 942836
Sacramento, CA 94236-0001



Untitled Document

 Water Quality Evaluation Section

Port of Stockton Monitoring Program Metadata


I. Contact Information

Program Manager: Shaun Philippart

Lead contact: Shaun Philippart
Senior Environmental Scientist
Department of Water Resources – North Central Region Office
3500 Industrial Blvd., West Sacramento 95691
Office: (916) 376-9661
Cell: (916) 208-2759

DWR Bryte Chemical Laboratory
1450 Riverbank Road,
West Sacramento, CA 95605
(916) 375-6008

Sid Fong: Supervisor of Bryte Chemical Laboratory

II. Study Area and Sample Site Objectives

A. General Information

During the summer, the Stockton Deep Water Ship Channel (DWSC) experiences low levels of dissolved oxygen (DO), below water quality objectives stated in the Water Quality Control Plan for the Sacramento River Basin and the San Joaquin River Basin. Because of the low DO concentrations, the Central Valley Regional Water Quality Control Board wrote up a Basin Plan Amendment and corresponding Staff Report assigning a Total Maximum Daily Load (TMDL) and assigning responsibility to various stakeholders. Within the staff report, staff cited “three main factors contributing to this DO impairment”. These reasons for low DO were channel geometry, loading of oxygen demanding substances and decreased flow through the DWSC.

The California Department of Water Resources installed a demonstration aeration facility to increase dissolved oxygen levels so that the criterion would be met. DO concentrations are not to go below 5.0 mg/L December through August and 6.0 mg/L from September through November.

WQE staff began continuous monitoring of four sites surrounding the output of the demonstration aerator within the DWSC beginning December 2006 and January 2007. We used continuous water quality monitoring sondes to measure several parameters, including temperature and dissolved oxygen. The data will be used to determine the effectiveness of the aeration facility on DO levels in the DWSC.

B. Name and Location Information for Continuous Water Quality Sampling Sites

- Port of Stockton Stations Map

C. Station Period of Record, Instrumentation, and Parameter Collection History

- Port of Stockton Stations Table

D.  CDEC and Water Data Library Station Codes

-CDEC and WDL Station Codes Table

III. Sampling Frequency

A. Sonde Instrument Sampling

There are a total of 4 Stockton Port water quality monitoring stations that collect time-series data at 15 minute intervals using either a YSI 6600EDS V2 or 600XLM internal data logging sonde. All stations record a single measurement of water temperature (Cº), dissolved oxygen (%), pH, specific conductance (µS/cm), and depth (m.), within the 15 minute interval. 

B. Field Instrument Sampling

Upon each site visitation (can vary from weekly to every two weeks), calibrated handheld field instruments are used to sample current water conditions and compare water quality  measurements to the YSI 6600EDS or 600XLM continuous monitoring stations. Temperature (Cº), pH, and specific conductance (µS/cm) measurements are field verified with an YSI 63 Handheld pH and Conductivity Instrument.  Dissolved oxygen measurements are field verified with a YSI Professional Optical Dissolved Oxygen Meter, and measurements are taken at 3ft., 6ft., 9ft., and 12ft. within the water column.

C. Discrete Sampling           

No discrete samples are taken at any of the four Port sites.

IV. Field Methods

A. Field measurements

During each site visit field readings are taken using portable and handheld instruments.  These handheld instruments are calibrated to comply with manufacturers or laboratory specifications.  Field readings are taken and recorded for comparison with YSI sonde data.  Field measurements are taken at 4 meter depths and dissolved oxygen measurements are taken at 3ft., 6ft., 9ft., and 12 ft. depths.

YSI 63 Handheld pH and Conductivity Instrument

The YSI 63 Handheld Instrument measures temperature, conductivity, pH, and salinity.  The instrument is calibrated once a month for conductivity and pH is calibrated before each field run.

YSI Professional Optical Dissolved Oxygen Meter

The YSI Professional Optical Dissolved Oxygen meter measures percent saturation and mg/L of dissolved oxygen.  The instrument is checked and calibrated before each field run.

V. Laboratory Methods

No laboratory samples are taken at any of the four Port sites.

VI. Data Management

A. Sonde Data

Post-deployment Quality Assurance
After the YSI 6600 sondes are removed from the field, DWR staff perform the following two procedures to check whether the sondes are still operating properly and measuring accurately:

  1. A post-deployment accuracy check on the day the sondes are removed and before the instruments are cleaned
  2. A comparison between the data measured by the handheld field instruments and the data collected by the sonde at the closest 15 minute time interval

The accuracy of sonde probes while deployed in the field can be negatively affected by probe malfunction, drift away from initial calibration, and/or fouling caused by biological growth on the probe reading surface.  DWR staff perform the post-deployment accuracy check by the following procedure prior to cleaning the sonde probes:

  1. Placing the sonde probes in fresh calibration standards with known values
  2. Operating the sondes in the standards and recording the values the sondes are reading
  3. Rating the values collected during the accuracy check for each constituent as excellent, good, fair, or poor based on their deviation from the calibration standard according to the USGS technical report “Guidelines and Standard Procedures for Continuous Water Quality Monitors-Station Operation, Record Computation, and Data Reporting” (Wagner et al., 2006)
    The ratings obtained from the accuracy check indicate the quality, accuracy, and reliability of the data that the sonde collected while in the field. 

In addition to the post-deployment accuracy check, DWR staff compare the water temperature, specific conductance, pH, dissolved oxygen, and turbidity data measured in the field by the handheld instruments (the YSI-63, YSI Pro-ODO, and HACH 2100P) to the sonde data that is closest in time.  While taking the field measurements, DWR staff attempt to collect the field readings at the same depth that the sonde probes are measuring at (1 meter) and as close to the sonde pipe as possible.  Since the field instruments are calibrated regularly, a large difference between the sonde and field readings could indicate inaccuracy of the sonde data during the deployment period.  DWR staff consider these comparisons between the field and sonde readings and the ratings obtained from the post-deployment accuracy check while assessing data quality when entering the continuous data into the Hydstra database. 

Data Quality Assurance/Quality Control (QA/QC)

DWR staff import data files from sondes into the North Central Region Office (NCRO) Hydstra database where additional QA/QC procedures are performed.  In addition to documenting the results of quality assurance procedures discussed in the previous section, staff use the results of these procedures to flag any suspect or unreliable data.  Any obvious outliers in the continuous dataset due to fouling or other factors are flagged as unreliable.  No data that has been determined by DWR staff as suspect or unreliable were used in this chapter; only reliable data of known good quality were used.  The reliable and good quality data in Hydstra are used to populate the Water Data Library where the data for all the continuous sites are available online at

B. Field Data

Field measurements are recorded on field data sheets upon each site visitation, and if the station has a discrete grab sample component, the data is then entered into the field module of DWR Bryte Laboratory’s “Flims” database.  Laboratory analyses are performed by DWR Bryte Laboratory on the discrete grab samples and the results are entered into the “FLIMS” database at the lab. For those stations without a discrete sample component, the field data sheets are used for sonde data comparison and archived accordingly.   On a regular basis the data from “Flims” database is loaded into DWR’s Water Data Library (WDL) database for public viewing and access.  Lab results are further archived and used for data report analyses.