Estuary Project | Research Methods II Final Exam Takla 1

Research Plan to Identify Causes of Complications Surrounding the San Francisco Bay Using Water Quality
Indicators of Dissolved Oxygen, Salinity, Temperature, and Chlorophyll-a

Julia Takla

Introduction (Addressing point A):

The San Francisco Bay, the largest pacific coast estuary, contains one of the world’s largest water

supply contributors: the federal Central Valley Project and the State Valley Project (Environmental

Protection Agency, 2022). Given that this estuary is one of the

most ecologically important contributors to the California region,

protection, and water quality monitoring are pertinent in order to

restore and maintain this key estuary on the west coast.

Unfortunately, a number of environmental determinants have

taken a toll on the watershed's ecological health with the list of

complications increasing due to population growth, pollution,

higher water demand, sewage spills, climate change, and small

droughts in the area (Environmental Protection Agency, 2022).

These factors must be monitored through water quality testing

and analyses.

The estuary is dominated by large urban cities such as San Francisco, San Jose, and Oakland,

affecting the physical, chemical, and biological characteristics of the estuary. To trace the large estuary

system, water begins by flowing from the Sacramento River, and the San Joaquin River Delta, and water

from the Sierra Nevada Mountains drains into the Suisun Bay. Subsequently, water from the Suisun Bay

flows into the Carquinez Strait along with the Napa River and enters the San Pablo Bay which flows

through the Golden Gate Strait and into the Pacific. The three major sub-embayments of the estuary are

San Pablo Bay, Central Bay, and South Bay. These bays, connected by Suisun Bay form rich habitat

diversity to support marine and coastal organisms (Smithsonian, n.d.). This complex, large water system
Estuary Project | Research Methods II Final Exam Takla 2

characterized as the San Francisco Bay, contains marshes and mudflats along the coast that provide food

and shelter for wildlife in the San Francisco area, specifically, about 500 species of fish, birds, mammals,

amphibians, and invertebrates (SF Ecosystem, 2020). The San Francisco Bay provides a feeding area and

wintering ground for millions of birds and supports ⅔ of California’s salmon (SF Ecosystem,

2022)(Smithsonian, n.d.). Unfortunately, more and more nonnative species are being introduced into the

estuary over the last few decades leading to a change in the biological, chemical, and physical

characteristics of the watershed.

Crumbling sewage infrastructure and sewage spills are becoming a cause of a sharp increase in

bacteria and toxicity; 40% of the aquatic ecosystem has been eliminated in San Francisco Bay due to

habitat destruction in the last 150 years (Environmental Protection Agency, 2022). Over the past few

years, droughts, rising sea levels, sewage spills, flooding, and pollution have accumulated several

challenges listed by the EPA in order to set goals for minimization and mitigation. This includes high

pesticide concentrations such as diazinon and DDT, high metal concentrations such as mercury, zinc, and

selenium, manufacturing compounds, pathogenic outbreaks, nutrients, low dissolved oxygen (DO),

exotic species, salinity impairments, and temperature toxicity from unknown sources (Environmental

Protection Agency, 2022). These challenges pose a threat to the ecological and environmental benefits

the estuary has previously provided for a number of native species and water supply. Therefore, testing

for DO as the first water quality indicator is wholly pertinent in order to determine the ability of the

tributary or estuarine habitat to support aquatic life. Previous trends of the San Francisco Bay have

shown relatively low DO levels which is why a continuous monitoring of this parameter is pivotal to

identifying unsupported areas in parts of the estuary. Depleted DO can be a potential indicator of

associated high pesticide concentrations and heavy metals targeting two of the previously listed

challenges. The second water quality indicator is salinity. Chinook salmon (Oncorhynchus tshawytscha),

previously a well-populated species of salmon in San Francisco Bay, has been affected by fluctuating
Estuary Project | Research Methods II Final Exam Takla 3

salinity levels. Given that the chinook salmon is a keystone species of the pacific west and its population

has been declining due to unknown reasons (doughts &

heat waves an accepted possibility), salinity observance

is crucial for the San Francisco estuary. Many chinook

salmon have been found washed up along the coast of

the estuary more recently with a number of various,

suspected causes. Temperature toxicity due to unknown

sources is another primary complication occurring in the

estuary. To determine the source, surveillance of

multiple parameters while simultaneously obtaining

temperature data values can help determine a correlation between one of the many potential factors.

However, a combination of multiple issues surrounding the bay could lead to temperature toxicity such

as DO levels, heavy metals/pesticides, manufacturing compounds, and pathogens. In more recent years,

algae blooms in San Francisco Bay have become more abundant due to eutrophication and high nitrate

and phosphate concentrations (Kamperin, 2018). Thus, the measurement of chlorophyll-a allows for

more direct monitoring of algae biomass concentration which can potentially tie into temperature and

low DO complications. Rather than stating the causes of these concerns to be inconclusive, measuring

and analyzing these water quality parameters concurrently could reveal possible associations and point

towards a larger cause. In order to obtain a full depiction of the data, sampling would occur at sites along

San Pablo Bay, Central Bay, and South Bay. By doing so, a broad area of data can be illustrated as

opposed to sampling from only the South Bay which is closest to the Golden Strait and the Pacific Ocean.

Methodology (Addressing Points B &D):

In this study, four water quality parameters would be tested in the San Francisco Bay:

temperature, salinity, dissolved oxygen, and chlorophyll-a. In order to identify causes and correlations for
 Estuary Project | Research Methods II Final Exam Takla 4

the concerns presented by the Environmental Protection Agency, these four parameters would reveal

good information regarding pesticide and heavy metal concentration, algae blooms, and chinook salmon

population deterioration.

Study Sites & Timeline:

In order to obtain more telling results, at least five

samples along the lower Sacramento River, lower San

Joaquin River Delta, Carquinez Strait, and Suisun Bay, and

10 sample sites along the San Pablo Bay, Central Bay, and

San Francisco South Bay. Each water quality parameter

(temperature, salinity, DO, & chlorophyll) would be

measured every other day for six months in order to

establish analyzed table trends and correlations. After

obtaining sufficient data, water quality contour maps can

be created to observe gradients and trends across San Francisco Bay.

Advanced Instruments & Cost Analysis:

Water Quality Parameter Instrument Name & Technological Cost Link

Advancement
https://www.amazon.com/RCYAGO-Smart-Bluetooth-Dissolved-Oxygen/dp/B09NLPD
Dissolved Oxygen RCYAGO Smart Bluetooth Dissolved Oxygen Meter: $99.99
4QM/ref=asc_df_B09NLPD4QM/?tag=hyprod-20&linkCode=df0&hvadid=5648027406

Accurate Bluetooth Data Transmission with 65&hvpos=&hvnetw=g&hvrand=10524003442072732581&hvpone=&hvptwo=&hvqm

t=&hvdev=c&hvdvcmdl=&hvlocint=&hvlocphy=9003992&hvtargid=pla-159991359470
multi-parameter display. Mobile phone application
4&psc=1

to save data.

https://www.amazon.com/RCYAGO-Smart-Bluetooth-Dissolved-Oxygen/dp/B09NLPD
Temperature *Measures Temp. as well* RCYAGO Smart —------
4QM/ref=asc_df_B09NLPD4QM/?tag=hyprod-20&linkCode=df0&hvadid=5648027406

Bluetooth Dissolved Oxygen Meter: Accurate 65&hvpos=&hvnetw=g&hvrand=10524003442072732581&hvpone=&hvptwo=&hvqm

t=&hvdev=c&hvdvcmdl=&hvlocint=&hvlocphy=9003992&hvtargid=pla-159991359470
Estuary Project | Research Methods II Final Exam Takla 5

4&psc=1
Bluetooth Data Transmission with multi-parameter

display. Mobile phone application to save data.

https://www.amazon.com/Refractometer-Fishkeeping-Automatic-Temperature-Comp
Salinity Salinity Refractometer for Marine Monitoring 0-100 $19.88
ensation/dp/B018LRO1SU/ref=asc_df_B018LRO1SU/?tag=hyprod-20&linkCode=df0&

PPT with Automatic Temperature Compensation: hvadid=198088359792&hvpos=&hvnetw=g&hvrand=10767959207833556249&hvpo

ne=&hvptwo=&hvqmt=&hvdev=c&hvdvcmdl=&hvlocint=&hvlocphy=9003992&hvtarg
made with chromium- very durable.
id=pla-319865121285&psc=1

Scilogex SP-V1000 Spectrophotometer: On-Board https://new.marshallscientific.com/Scilogex-SP-V1000-Spectrophotome

Chlorophyll-a
Data Storage: The System can save the test results,
up to 200 groups of data and 200 standard curves
$1440
ter-p/SCI-401021010009.htm?gclid=CjwKCAjwtcCVBhA0EiwAT1fY7yecG
U7l1EBdSqyoFEb9hq_TL1-SErr-FxV4q9lTQ98zrY8kgFDMvRoC_B4QAvD_
BwE

in the RAM memory.

Total Cost of Technologically Advanced Instruments: $1559.87

Analysis (Addressing Point C):

An estuary as large as the San Francisco Bay, requires meticulous sampling and monitoring

because of its influential ecological features and habitats. Identifying complications in the bay such as

high pesticide concentrations, high metal concentrations (mercury, zinc, selenium), manufacturing

compounds, pathogen impairments, excessive nutrients, low dissolved oxygen, exotic species, salinity

impairments, and temperature toxicity can lead to prevention and mitigation of such immense concerns.

Designing and establishing a concrete monitoring project to pinpoint and act upon the causes of these

changes is the appropriate course of action to be taken in order to maintain the populations that reside

in San Francisco Bay. The four water quality indicators chosen were temperature, dissolved oxygen,

salinity, and chlorophyll-a. To analyze the results of a six-month period of data collection, a scatter plot

should be constructed using each of the four parameters to determine if there is a correlation between

any two. If there is, it can reveal an association between two different variables or effects occurring in

San Francisco Bay. For instance, if chlorophyll-a concentrations appear to be high in the areas where DO
Estuary Project | Research Methods II Final Exam Takla 6

values are low, this associative pattern can hint toward algae blooms depleting the oxygen in that area.

To effectively analyze the results, water quality contour maps can be made to effectively observe each

variable in relation to location. With the data collected, an ANOVA test can be performed to determine

whether there are any statistically significant differences between the water quality parameters in the

different bays: San Pablo Bay, Central Bay, and San Francisco South Bay. Averages can be obtained from

the water quality parameters in each location and used to create a bar graph and Tukey post hoc graph

as a visual depiction of the differences. Upon performing all these statistical and graphical analyses, a

basis for action can be established for the San Francisco Bay water body authorities. This estuary

provides shelter, food, and habitat for hundreds of fish species, plant species, and millions of birds which

is why addressing high-priority complications is pivotal to sustaining this important watershed.

References

California Estuary Portal (n.d.). Retrieved from https://emp.opennrm.org/projects/11285

Environmental Protection Agency (2022). Retrieved from

https://www.epa.gov/sfbay-delta/what-are-challenges

Kamperin, A., & 21, J. (2020, July 22). Conservation of the San Francisco Bay. Retrieved from

https://richardsonbay.audubon.org/news/conservation-san-francisco-bay

McPhee, Megan (2009, January 02). How do spawning fish navigate back to the very same stream where

they were born? Retrieved from

https://www.scientificamerican.com/article/how-do-spawning-fish-navigate-back/

SF Ecosystem. (2018, October 13). Retrieved from

https://sfenvironment.org/ecosystems/overview/ecosystems#:~:text=The San Francisco Bay

supports,ground for millions of birds.

Stopping Stormwater Pollution in the Bay. (2021, December 14). Retrieved from
Estuary Project | Research Methods II Final Exam Takla 7

https://baykeeper.org/our-work/controlling-urban-storm-water-pollution

Tobias, J. (2020, April 21). The Extinction Crisis Devastating San Francisco Bay. Retrieved from

https://www.thenation.com/article/environment/extinction-san-francisco-bay/

WhippoR. (2017, July 11). San Francisco Bay, California. Retrieved from

https://marinegeo.si.edu/san-francisco-bay-california