Data Package Metadata View Summary

Six decades (1959-2021) of water quality in the upper San Francisco Estuary: an integrated database of 15 discrete monitoring surveys in the Sacramento San Joaquin Delta, Suisun Bay, Suisun Marsh, and San Francisco Bay

General Information

Data Package:

Local Identifier:

edi.750.1

Title:

Six decades (1959-2021) of water quality in the upper San Francisco Estuary: an integrated database of 15 discrete monitoring surveys in the Sacramento San Joaquin Delta, Suisun Bay, Suisun Marsh, and San Francisco Bay

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

The upper San Francisco Estuary (SFE) is simultaneously a central hub of water delivery in California and home to commercially important and endangered fishes, such as Chinook Salmon, Green Sturgeon, and Delta and Longfin Smelt. Extensive ecological monitoring has been conducted for over 50 years, mainly under the auspices of the Interagency Ecological Program for the San Francisco Estuary (https://iep.ca.gov/). We integrated water quality data from 15 boat-based long-term monitoring surveys in the upper SFE. This integrated dataset includes measurements of temperature (surface and bottom), conductivity (surface), salinity (surface), Secchi depth, qualitative concentration of the toxic alga Microcystis (surface), and Chlorophyll-a concentration (surface) from 1959 - 2021. The component surveys range in sampling frequency from thrice weekly to monthly and range in duration from 5 – 60 years. Most component surveys sample at fixed stations, but the Enhanced Delta Smelt Monitoring survey uses random sites and some stations (with “EZ” in the station name) of the Environmental Monitoring Program follow the salinity field. It is highly recommended to inspect the documentation of the component surveys for more information on their methods.

Publication Date:

2022-03-08

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

1959-06-13

End:

2022-08-25

People and Organizations
Contact:	Bashevkin, Samuel M (Delta Science Program, Delta Stewardship Council) [ email ]
Creator:	Bashevkin, Samuel M (Delta Science Program, Delta Stewardship Council)
Creator:	Perry, Sarah E (CA Department of Water Resources)
Creator:	Stumpner, Elizabeth B (USGS-CAWSC)

Data Entities
Data Table Name:	Delta_Integrated_WQ.csv
Description:	Integrated water quality database
Data Table Name:	Delta_Integrated_WQ_metadata.csv
Description:	Information on each survey included in the integrated database

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/750/1/6c5f35b1d316e39c8de0bfadfb3c9692
Name:	Delta_Integrated_WQ.csv
Description:	Integrated water quality database
Number of Records:	317274
Number of Columns:	51

Table Structure

Object Name:

Delta_Integrated_WQ.csv

Size:

74896892 bytes

Authentication:

7aa03fc32d266bb788f08a68b86aeb2b Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

Source

Station

Latitude

Longitude

Field_coords

Date

Datetime

Depth

Sample_depth_surface

Sample_depth_nutr_surface

Sample_depth_bottom

Tide

Temperature

Temperature_bottom

Conductivity

Conductivity_bottom

Salinity

Salinity_bottom

Secchi

Microcystis

Chlorophyll_Sign

Chlorophyll

DissolvedOxygen

DissolvedOxygen_bottom

DissolvedOxygenPercent

DissolvedOxygenPercent_bottom

pH_bottom

TotAlkalinity

TotAmmonia

DissAmmonia_Sign

DissAmmonia

DissBromide

DissCalcium

TotChloride

DissChloride

DissNitrateNitrite_Sign

DissNitrateNitrite

DOC

TOC

DON

TON

DissOrthophos_Sign

DissOrthophos

TotPhos

DissSilica

TDS

TSS

VSS

TKN

Notes

Definition:

Survey from which data originated

Identifier for the sampling station

Latitude where sample was collected

Longitude where sample was collected

Do the Latitude and Longitude coordinates represent field-collected coordinates at the time of sample collection?

Date sample was collected (America/Los_Angeles timezone)

Date and time when sample was collected (America/Los_Angeles timezone)

Bottom depth at the location the sample was collected. This can be either a depth measured at the time of sample collection or the average water depth for the sampling station, depending on the survey.

Depth below surface at which the surface samples were collected

Depth below surface of the surface nutrient sample. This is only used for the USGS_SFBS survey, in which nutrients were sometimes collected at a deeper depth than the shallowest water quality samples

Depth below surface at which the bottom temperature measurement was taken

Tidal stage

Surface water temperature

Bottom water temperature

Surface specific conductivity

Bottom specific conductivity

Surface salinity

Bottom salinity

Secchi depth (NOTE data are right censored in certain time periods, since in some cases the disk was still visible at the deepest depth to which it could be extended

Qualitative abundance of the toxic microalga Microcystis

Whether the Chlorophyll value is lower than reported (< because it is below the reporting limit and the reporting limit is used as the value), estimated ~ (extrapolated at low end), or reported as the measured value =.

Chlorophyll-a concentration at surface. For USGS_CAWSC data, if Chlorophyll_Sign is <, this value is equal to the reporting limit and if Chlorophyll_Sign is ~ then this value is estimated (extrapolated at low end). Otherwise this value is the actual measured value.

Dissolved oxygen at surface.

Dissolved oxygen at bottom.

Dissolved oxygen percent at surface.

Dissolved oxygen percent at bottom.

pH at surface

pH at bottom

Total Alkalinity

Total Ammonia

Whether the DissAmmonia value is lower than reported (< because it is below the reporting limit and the reporting limit is used as the value), estimated ~, or reported as the measured value =.

Dissolved Ammonia. For EMP and USGS_CAWSC data, if DissAmmonia_Sign is <, this value is equal to the reporting limit. For USGS_CAWSC data, if DissAmmonia_Sign is ~ then this value is estimated. Otherwise this value is the actual measured value.

Dissolved bromide

Dissolved calcium

Total chloride

Dissolved chloride

Whether the DissNitrateNitrite value is lower than reported (< because it is below the reporting limit and the reporting limit is used as the value), estimated ~, or reported as the measured value =.

Dissolved Nitrate and Nitrite. For EMP and USGS_CAWSC data, if DissNitrateNitrite_Sign is <, this value is equal to the reporting limit. For USGS_CAWSC data, if DissNitrateNitrite_Sign is ~ then this value is estimated. Otherwise this value is the actual measured value.

Dissolved organic carbon

Total organic carbon

Dissolved organic nitrogen

Total organic nitrogen

Whether the DissOrthophos value is lower than reported (< because it is below the reporting limit and the reporting limit is used as the value), estimated ~, or reported as the measured value =.

Dissolved Ortho-phosphate. For EMP and USGS_CAWSC data, if DissOrthophos_Sign is <, this value is equal to the reporting limit. For USGS_CAWSC data, if DissOrthophos_Sign is ~ then this value is estimated. Otherwise this value is the actual measured value.

Total phosphorous

Dissolved Silica

Total dissolved solids

Total suspended solids

Volatile suspended solids

Total Kjeldahl nitrogen

Any notes recorded during sampling

Storage Type:

string

float

string

date

float

string

float

string

float

string

float

string

float

string

float

string

Measurement Type:

nominal

ratio

nominal

dateTime

ratio

nominal

ratio

nominal

ratio

nominal

ratio

nominal

ratio

nominal

ratio

nominal

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	20mm
Definition	20-mm Survey
Source

Code Definition

Code	Baystudy
Definition	San Francisco Bay Study
Source

Code Definition

Code	DJFMP
Definition	Delta Juvenile Fish Monitoring Program
Source

Code Definition

Code	EDSM
Definition	Enhanced Delta Smelt Monitoring
Source

Code Definition

Code	EMP
Definition	Environmental Monitoring Program
Source

Code Definition

Code	FMWT
Definition	Fall Midwater Trawl
Source

Code Definition

Code	SDO
Definition	Stockton Dissolved Oxygen Monitoring
Source

Code Definition

Code	SKT
Definition	Spring Kodiak Trawl
Source

Code Definition

Code	SLS
Definition	Smelt Larva Survey
Source

Code Definition

Code	STN
Definition	Summer Townet Survey
Source

Code Definition

Code	Suisun
Definition	Suisun Marsh Fish Study
Source

Code Definition

Code	USBR
Definition	USBR Sacramento Deepwater Shipping Channel Survey
Source

Code Definition

Code	USGS_SFBS
Definition	USGS San Francisco Bay Survey
Source

Code Definition

Code	YBFMP
Definition	Yolo Bypass Fish Monitoring Program
Source

Code Definition

Code	USGS_CAWSC
Definition	USGS California Water Science Center discrete water quality data
Source

Definition

Identifier for the sampling station

Unit	degree
Type	real
Min	37.471667
Max	38.97131

Unit	degree
Type	real
Min	-122.471667
Max	-121.00969

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	FALSE
Definition	Coordinates were not recorded in the field. These coordinates represent the target location (e.g., location of the fixed sampling station).
Source

Code Definition

Code	TRUE
Definition	Coordinates were recorded in the field and represent the exact location the sample was collected
Source

Format	YYYY-MM-DD
Precision

Format	YYYY-MM-DD hh:mm:ss
Precision

Unit	meter
Type	real
Min	0
Max	41.1

Unit	meter
Type	real
Min	0.070104
Max	1.5

Unit	meter
Type	real
Min	0.5
Max	4

Unit	meter
Type	real
Min	1.3347192
Max	80

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Ebb
Definition	Ebb tide
Source

Code Definition

Code	Flood
Definition	Flood tide
Source

Code Definition

Code	High Slack
Definition	High Slack tide
Source

Code Definition

Code	Low Slack
Definition	Low Slack tide
Source

Code Definition

Code	Overtopping
Definition	Periods of floodplain inundation that drown out tidal effects. Only used by YBFMP
Source

Unit	celsius
Type	real
Min	1.32
Max	38

Unit	celsius
Type	real
Min	5.28
Max	80.6

Unit	microSeimenPerCentimeter
Type	real
Min	5
Max	189013

Unit	microSeimenPerCentimeter
Type	real
Min	77.7
Max	45856

Unit	dimensionless
Type	real
Min	0
Max	162.076718289885

Unit	dimensionless
Type	real
Min	0.0355135314010307
Max	29.7162599830951

Unit	centimeter
Type	real
Min	0
Max	5000

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1
Definition	absent
Source

Code Definition

Code	2
Definition	low
Source

Code Definition

Code	3
Definition	medium
Source

Code Definition

Code	4
Definition	high
Source

Code Definition

Code	5
Definition	very high
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	<
Definition	Below reporting limit. The value in the corresponding column represents the reporting limit, not the actual measured value (since the measured value was below the reporting limit and thus could not be measured). If the value in the correspondinc column is NA, the reporting value is unknown and the true value is below it.
Source

Code Definition

Code	=
Definition	The value in the corresponding column is the true mesasured value because the measured value was at or above the reporting limit
Source

Code Definition

Code	~
Definition	The value in the corresponding column is estimated.
Source

Unit	microgramsPerLiter
Type	real
Min	-0.3
Max	498.57

Unit	milligramsPerLiter
Type	real
Min	0.1
Max	22.3

Unit	milligramsPerLiter
Type	real
Min	6.14
Max	11.12

Unit	dimensionless
Type	real
Min	73.9
Max	135.9

Unit	dimensionless
Type	real
Min	73.2
Max	118.4

Unit	dimensionless
Type	real
Min	6.1
Max	10.7

Unit	dimensionless
Type	real
Min	6.89
Max	9.03

Unit	milligramsPerLiter
Type	real
Min	29
Max	126

Unit	milligramsPerLiter
Type	real
Min	0.01
Max	2.6

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	<
Definition	Below reporting limit. The value in the corresponding column represents the reporting limit, not the actual measured value (since the measured value was below the reporting limit and thus could not be measured). If the value in the correspondinc column is NA, the reporting value is unknown and the true value is below it.
Source

Code Definition

Code	=
Definition	The value in the corresponding column is the true mesasured value because the measured value was at or above the reporting limit
Source

Code Definition

Code	~
Definition	The value in the corresponding column is estimated.
Source

Unit	milligramsPerLiter
Type	real
Min	0
Max	6.373185

Unit	milligramsPerLiter
Type	real
Min	0.01
Max	97

Unit	milligramsPerLiter
Type	real
Min	4
Max	724

Unit	milligramsPerLiter
Type	natural
Min	1
Max	16300

Unit	milligramsPerLiter
Type	real
Min	2
Max	19200

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	<
Definition	Below reporting limit. The value in the corresponding column represents the reporting limit, not the actual measured value (since the measured value was below the reporting limit and thus could not be measured). If the value in the correspondinc column is NA, the reporting value is unknown and the true value is below it.
Source

Code Definition

Code	=
Definition	The value in the corresponding column is the true mesasured value because the measured value was at or above the reporting limit
Source

Code Definition

Code	~
Definition	The value in the corresponding column is estimated.
Source

Unit	milligramsPerLiter
Type	real
Min	0.00014007
Max	15.2

Unit	milligramsPerLiter
Type	real
Min	0.068
Max	100

Unit	milligramsPerLiter
Type	real
Min	0.063
Max	12.3

Unit	milligramsPerLiter
Type	real
Min	0.1
Max	3

Unit	milligramsPerLiter
Type	real
Min	0.1
Max	3.4

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	<
Definition	Below reporting limit. The value in the corresponding column represents the reporting limit, not the actual measured value (since the measured value was below the reporting limit and thus could not be measured). If the value in the correspondinc column is NA, the reporting value is unknown and the true value is below it.
Source

Code Definition

Code	=
Definition	The value in the corresponding column is the true mesasured value because the measured value was at or above the reporting limit
Source

Code Definition

Code	~
Definition	The value in the corresponding column is estimated.
Source

Unit	milligramsPerLiter
Type	real
Min	0.00371688
Max	8

Unit	milligramsPerLiter
Type	real
Min	0.02
Max	2.6

Unit	milligramsPerLiter
Type	real
Min	0.00060084
Max	73

Unit	milligramsPerLiter
Type	natural
Min	50
Max	38780

Unit	milligramsPerLiter
Type	real
Min	1
Max	342

Unit	milligramsPerLiter
Type	real
Min	1
Max	64

Unit	milligramsPerLiter
Type	real
Min	0.1
Max	12

Definition

Any notes recorded during sampling

Missing Value Code:

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Time not recorded

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured. This is only used for USGS_SFBS data

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured. This is only used for USGS_CAWSC data

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured. If the DissAmmonia_Sign value is <, then the reporting limit is unknown and this value is below the reporting limit.

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured. If the DissNitrateNitrite_Sign value is <, then the reporting limit is unknown and this value is below the reporting limit.

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured. If the DissOrthophos_Sign value is <, then the reporting limit is unknown and this value is below the reporting limit.

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Code	NA
Expl	Unknown or not measured

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/750/1/0f71269d5347e1c4318424f7efda7503
Name:	Delta_Integrated_WQ_metadata.csv
Description:	Information on each survey included in the integrated database
Number of Records:	15
Number of Columns:	10

Table Structure

Object Name:

Delta_Integrated_WQ_metadata.csv

Size:

2570 bytes

Authentication:

5c3e00f434e1eeac69bd23c4f4750111 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

Survey

Abbreviation

Agency

Survey_focus

Start_year

Season

Frequency

Data_source

Surface_sample_depth

Bottom_sample_depth

Definition:

Name of the monitoring survey

Abbreviation of the monitoring survey name

Lead agency for the monitoring survey

Primary focus of the monitoring survey

First year data were collected

Months in which data are primarily collected, although some sampling may have occurred outside the indicated months

Normal frequency of sampling, although this has changed over time for many of the surveys

Raw data source

Depth below surface at which surface water samples were collected. Surface bucket indicates samples collected by scooping water with a bucket from the surface. recorded indicates that the actual depth of the sample (from the surface) is recorded in the dataset in Sample_depth_surface.

Depth above the bottom at which bottom temperature data were generally collected. recorded indicates that the actual depth of the sample (from the surface) is recorded in the dataset in Sample_depth_bottom.

Storage Type:

string

date

string

Measurement Type:

nominal

dateTime

nominal

Measurement Values Domain:

Definition

Name of the monitoring survey

Definition

Abbreviation of the monitoring survey name

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	CDFW
Definition	California Department of Fish and Wildlife
Source

Code Definition

Code	DWR
Definition	California Department of Water Resources
Source

Code Definition

Code	UC Davis
Definition	University of California, Davis
Source

Code Definition

Code	USBR
Definition	United States Bureau of Reclamation
Source

Code Definition

Code	USFWS
Definition	United States Fish and Wildlife Service
Source

Code Definition

Code	USGS
Definition	United States Geological Survey
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Fish
Definition	Survey focused primarily on monitoring fish
Source

Code Definition

Code	Water quality
Definition	Survey focused primarily on monitoring water quality
Source

Format	YYYY
Precision

Definition

Months in which data are primarily collected, although some sampling may have occurred outside the indicated months

Definition

Normal frequency of sampling, although this has changed over time for many of the surveys

Definition

Raw data source

Definition

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data (\"Data User\" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available \"as is.\" The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
https://vocab.lternet.edu/	estuaries, water quality, water temperature, secchi depth, algae, chlorophyll a, specific conductivity, salinity, surveys, long term monitoring, nutrients
(No thesaurus)	data integration

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package

Description:

1. Introduction

To create an integrated database of discrete water quality measurements in the San Francisco Estuary, we combined data from 15 boat-based surveys with the R statistical programming language (R Core Team 2020). The data integration code was packaged into the R package discretewq v2.3.1: https://github.com/sbashevkin/discretewq (Bashevkin et al. 2022).

The surveys included in the integrated database are long-term monitoring surveys managed by federal agencies, state agencies, and the University of California, Davis. Eight surveys are primarily focused on collecting fish abundance data but collect water quality data alongside fish samples. These include the California Department of Fish and Wildlife (CDFW) Fall Midwater Trawl (FMWT), CDFW Summer Townet Survey (STN), CDFW Spring Kodiak Trawl (SKT), CDFW 20-mm Survey (20mm), CDFW San Francisco Bay Study (Baystudy), CDFW Smelt Larva Survey (SLS), California Department of Water Resources (DWR) Yolo Bypass Fish Monitoring Program (YBFMP), United States Fish and Wildlife Service (USFWS) Enhanced Delta Smelt Monitoring (EDSM), USFWS Delta Juvenile Fish Monitoring Program (DJFMP), and University of California, Davis Suisun Marsh Fish Study (Suisun). An additional 4 surveys are primarily focused on water quality data: the DWR Environmental Monitoring Program (EMP), DWR Stockton Dissolved Oxygen Survey (SDO), United States Bureau of Reclamation Sacramento Deepwater Shipping Channel Survey (USBR), the United States Geological Survey (USGS) San Francisco Bay Survey (USGS_SFBS), and the USGS California Water Science Center monitoring (USGS_CAWSC) (see Delta_Integrated_WQ_metadata.csv).

The primary aim of this data integration was to combine datasets to facilitate analyses of water quality trends in the upper San Francisco Estuary. The focal water quality variables included water temperature, conductivity (or salinity), Secchi depth, Microcystis concentration, and chlorophyll concentration. Key nutrient variables were retained from the USGS_SFBS, USGS_CAWSC, and EMP surveys. These variables were all collected from the surface of the water column. In addition, water temperature from the bottom of the water column was retained when available. Not all surveys measured all focal variables. Some surveys (particularly the water quality surveys) measured more water quality variables than were retained in this integrated dataset.

While we describe some of the methods here, it is highly recommended to inspect the documentation of the component surveys (see provenance and below for citations) for more information on their methods.

2. Survey methods

Methods for measuring water quality variables were generally consistent among the component surveys, but there were slight differences. All surface water samples were collected within the upper 1 m, but the exact depth differed slightly among studies. USGS_SFBS collected some surface temperatures at depths of 2 m, but we only retained samples collected at 1 m or shallower for compatibility with the other studies. The only exception to this is for nutrient data collected by the USGS_SFBS survey. Nutrient samples were sometimes collected deeper than the surface water quality data. In these cases, we selected the shallowest nutrient data available. The maximum depth of surface nutrient data is 4 m and these depths are available in the dataset. Bottom temperature samples were collected within 1 m of the bottom (see Delta_Integrated_WQ_metadata.csv). More detailed methods and protocols for most component surveys can be found in the data source links in Delta_Integrated_WQ_metadata.csv or the provenance citations.

2.1. Water temperature

While all surveys now measure water temperature with digital sensors, older surveys used less precise handheld thermometers in earlier years. More precise sensors were first used by FMWT in 1995, STN in 1994, and DJFMP in 2014. All other surveys used more precise methods to measure temperature since inception. SKT had notes on some temperature records that they were transcribed from a different monitoring program (CDEC) so these values were all removed.

2.2. Conductivity/Salinity

Most surveys reported specific conductivity except USGS_SFBS which reported salinity. DJFMP and EDSM could not verify their conductivity metric for data collected before June 2019 so conductivity values collected before that date are removed from the integrated dataset.

2.3. Secchi depth

Secchi depth was measured on the shady side of the boat (when possible) in all surveys that measured this variable. It is important to note that the Secchi data are right-censored, since in some cases the disk was still visible at the deepest depth to which it could be extended. In these cases, the maximum extension depth was usually recorded, even if the disk was still visible.

2.4. Microcystis

Concentration of the toxic microalga Microcystis was measured on the same 5-point qualitative scale (absent, low, medium, high, very high) by the 3 surveys that measured this variable. For a short period of time (2012-15), FMWT added a 6^th level to the Microcystis scale to represent Microcystis presence in zooplankton net cod-ends. Outside this short time period, this was measured as a “low” on the 5-point scaled, so all records of this 6^th level were converted to “low” for consistency with other surveys and time periods.

2.5. Chlorophyll

Chlorophyll-a methods differed slightly among surveys. EMP filtered water samples through a 1 µm glass fiber filter and measured Chlorophyll concentrations in the lab. USBR and USGS_SFBS used sonde probes to measure chlorophyll in the field but USGS_SFBS calibrated these field measurements with filtered water samples collected and analyzed similar to EMP.

2.6. Nutrients

EMP collected and preserved nutrients samples in accordance with standard protocols (Interagency Ecological Program et al. 2021a), after which they were processed in a lab. Nutrients were filtered in the field when applicable. USGS_SFBS collected, preserved, and processed dissolved inorganic nutrients in a similar manner to EMP. Both surveys collected water using a fixed flow-through pump.

3. Data integration methods

From each dataset, we selected columns corresponding to the water quality variables of interest as well as important accessory information (date, time, station, latitude, longitude, depth, tide, and any notes). We then renamed variables for consistency and converted all variables to consistent units. Salinity was calculated from specific conductivity using the ec2pss function from the wql R package (Jassby et al. 2017). This function uses the Practical Salinity Scale 1978 for salinities between 2 and 42 (Fofonoff and Millard Jr 1983) and the extension of the Practical Salinity Scale (Hill et al. 1986) for salinities below 2. Conductivity data were also retained in the integrated dataset. In most cases, latitude and longitude coordinates of the fixed sampling stations were retained. When these coordinates were not available (e.g. for non-fixed stations), we retained any coordinates that were recorded during the field sampling. To remove duplicate values from the dataset, only one set of values was retained for each recorded date, time, and location. All data integration code can be found in the discretewq R package v2.3.1 (https://github.com/sbashevkin/discretewq; Bashevkin et al. 2022).

4. Literature cited

Bashevkin, S. M., S. E. Perry, and E. B. Stumpner. 2022. discretewq: An Integrated Dataset of Discrete Water Quality in the San Francisco Estuary v2.3.1. Zenodo. doi:10.5281/zenodo.6335814

Fofonoff, N. P., and R. C. Millard Jr. 1983. Algorithms for the computation of fundamental properties of seawater. UNESCO Technical Papers in Marine Science 44.

Hill, K., T. Dauphinee, and D. Woods. 1986. The extension of the Practical Salinity Scale 1978 to low salinities. IEEE Journal of Oceanic Engineering 11: 109–112.

Jassby, A. D., J. E. Cloern, and J. Stachelek. 2017. wql: Exploring Water Quality Monitoring Data.

R Core Team. 2020. R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing.

5. Data sources

CDFW. 2021a. Fall Midwater Trawl data. https://filelib.wildlife.ca.gov/Public/TownetFallMidwaterTrawl/FMWT%20Data/.

CDFW. 2021b. Summer Townet data. https://filelib.wildlife.ca.gov/Public/TownetFallMidwaterTrawl/TNS%20MS%20Access%20Data/TNS%20data/.

CDFW. 2021c. Bay Study data. https://filelib.wildlife.ca.gov/Public/BayStudy/.

Cloern, J. E., and T. S. Schraga. 2016. USGS Measurements of Water Quality in San Francisco Bay (CA), 1969-2015 (ver. 3.0 June 2017). U. S. Geological Survey data release. doi:https://doi.org/10.5066/F7TQ5ZPR

Interagency Ecological Program, L. Damon, and A. Chorazyczewski. 2021a. Interagency Ecological Program San Francisco Estuary 20mm Survey 1995 - 2021. ver 4. Environmental Data Initiative. doi:10.6073/pasta/32de8b7ffbe674bc6e79dbcd29ac1cc2

Interagency Ecological Program, L. Damon, and A. Chorazyczewski. 2021b. Interagency Ecological Program San Francisco Estuary Spring Kodiak Trawl Survey 2002 - 2021. ver4. Environmental Data Initiative. doi:10.6073/pasta/f0e2916f4a026f3f812a0855cee74a8d

Interagency Ecological Program, L. Damon, T. Tempel, and A. Chorazyczewski. 2021c. Interagency Ecological Program San Francisco Estuary Smelt Larva Survey 2009 – 2021. ver 4. Environmental Data Initiative. doi:10.6073/pasta/8e1ceb1c02fbc8b0ba7a6b58229109f2

Interagency Ecological Program, S. Lesmeister, and J. Rinde. 2020a. Interagency Ecological Program: Discrete dissolved oxygen monitoring in the Stockton Deep Water Ship Channel, collected by the Environmental Monitoring Program, 1997-2018. ver 2. Environmental Data Initiative. doi:10.6073/PASTA/3268530C683726CD430C81894FFAD768

Interagency Ecological Program, M. Martinez, and S. Perry. 2021d. Interagency Ecological Program: Discrete water quality monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 1975-2020. ver 4. Environmental Data Initiative. doi:10.6073/pasta/31f724011cae3d51b2c31c6d144b60b0

Interagency Ecological Program, R. McKenzie, J. Speegle, A. Nanninga, and J. Hagen. 2021e. Interagency Ecological Program: Over four decades of juvenile fish monitoring data from the San Francisco Estuary, collected by the Delta Juvenile Fish Monitoring Program, 1976-2021. ver 8. Environmental Data Initiative. doi:10.6073/pasta/8dfe5eac4ecf157b7b91ced772aa214a

Interagency Ecological Program, C. L. Pien, J. B. Adams, and N. Kwan. 2020b. Interagency Ecological Program: Zooplankton catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2018. ver 2. Environmental Data Initiative. doi:10.6073/pasta/baad532af96cba1d58d43b89c08ca081

Interagency Ecological Program, B. Schreier, B. Davis, and N. Ikemiyagi. 2019. Interagency Ecological Program: Fish catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2018. ver 2. Environmental Data Initiative. doi:10.6073/PASTA/B0B15AEF7F3B52D2C5ADC10004C05A6F

O’Rear, T., J. Durand, and P. Moyle. 2021. Suisun Marsh Fish Study. https://watershed.ucdavis.edu/project/suisun-marsh-fish-study.

Schraga, T. S., E. S. Nejad, C. A. Martin, and J. E. Cloern. 2018. USGS measurements of water quality in San Francisco Bay (CA), beginning in 2016 (ver. 3.0, March 2020). U. S. Geological Survey data release. doi:https://doi.org/10.5066/F7D21WGF

United States Fish And Wildlife Service, T. Senegal, R. Mckenzie, and others. 2021. Interagency Ecological Program and US Fish and Wildlife Service: San Francisco Estuary Enhanced Delta Smelt Monitoring Program data, 2016-2021. ver 7. Environmental Data Initiative. doi:10.6073/pasta/65f9297a7077320f4ba31c2acd685f93

USBR, R. Dahlgren, L. Loken, and E. Van Nieuwenhuyse. 2020. Monthly vertical profiles of water quality in the Sacramento Deep Water Ship Channel 2012-2019.

U.S. Geological Survey. 2022. USGS water data for the Nation: U.S. Geological Survey National Water Information System database, accessed February 7, 2022, at https://doi.org/10.5066/F7P55KJN

Description:

This method step describes provenance-based metadata as specified in the LTER EML Best Practices.