GEOLOGICAL SURVEY CIRCULAR 637 -A, B 

A Preliminary Study of the 

Effects of Water Circulation in the 

San Francisco Bay Estuary 

Prepared in cooperation with the U.S. Department of Housing and Urban Development 

A Preliminary Study of the 

Effects of Water Circulation in the 

San Francisco Bay EstuarySome Effects of Fresh-water Inflow 

on the Flushing of South 

San Francisco Bay 

By D. S. McCulloch, D. H. Peterson, P. R. Carlson, and T. J. Conomos 

Movement of Seabed Drifters in 

the San Francisco Bay Estuary 

and the Adjacent Pacific Ocean 

By T. J. Conomos, D. H. Peterson, P. R. Carlson, and D. S. McCulloch 

G E 0 l 0 G I C A l S U R V E Y C I R C U l A R 6 3 7- A, B 

Prepared in cooperation with the 

U.S. Department of Housing and 

Urban Development 

Washington 1970 
United States Department of the Interior 

WALTER J. HICKEL, Secretary 

Geological Survey 

William T. Pecora, Director 

Free on application to the U.S. Geological Survey, Washington, D.C. 20242 
FOREWORD 

There is a growing national awareness of the value of major 

estuaries like San Francisco Bay as important coastal assets and 

an appreciation for the complicated natural processes that take 

place within them. We must understand these natural systems 

better in order to respond to competing demands for the use of 

an estuary. 

The millions of people in the cities that surround San 

Francisco Bay depend in one way or another upon the water in the 

bay for recreation, commerce, waste emplacement, biota balances, 

or aesthetic enjoyment. Such uses are contingent in varying 

degree upon the rate with which human or natural processes add 

materials to or remove them from the estuary. The purpose of 

this report is to provide information that will lead to a better 

understanding of the ecosystem of San Francisco's south bay, to 

indicate significant geochemical balances, to help predict consequences of man's activities, to suggest solutions to existing 

or potential problems, and to insure wise use of this invaluable 

natural resource. 

Water-quality characteristics of south bay are influenced 

primarily by inflow of fresh water, manmade wastes, and tidal exchanges of water of varying salinity. Changes in any of these 

controls could have significant effects on the overall quality of 

the bay. This report qualitatively demonstrates that high and 

low seasonal inflows of fresh water to the bay's Sacramento 

River delta correlate inversely with salinity and phosphate concentration in the south bay. It suggests that net fresh water 

flow to the bay from this source is a major quality control 

under present conditions. Additional investigations are warranted to establish long-term significance of this suggested 

coupling. 

} M.J:c,cA't,.C..-

w. T. Pecora, 

Director 

III 

Some Effects of Fresh-water Inflow 

on the Flushing of South 

San Francisco Bay: 

A Preliminary Report 

By D. S. McCulloch, D. H. Peterson, P. R. Carlson, and T. J. Conomos 

A PRELIMINARY STUDY OF THE EFFECTS OF WATER CIRCULATION 

IN THE SAN FRANCISCO BAY ESTUARY 

GEOLOGICAL SURVEY CIRCULAR 637-A 

Prepared in cooperation with the 

U.S. Department of Housing and 

Urban Development 

CONTENTS 

Page 

Introduction --------------------------------------------------------- Al 

Salinity ------------------------------------------------------------- 3 

Flushing of the south bay---------------------------------------------- 13 

Phosphate ----------------------------------------------------------- 15 

Summary------------------------------------------------------------ 18 

Appendix ------------------------------------------------------------ 20 

ILLUSTRATIONS 

Page 

Figure 1. Index map of the San Francisco Bay estuary showing locations of water 

sampling stations ---------------------------------------------------------------- A2 

2. Graph showing comparison of the salinity changes at two stations in the 

south bay and the Golden Gate with the combined discharge of the Sacramento and San Joaquin Rivers and the combined discharge of the 

south-bay streams and sewage effluent --------.:..------------------------------------ 4 

3. Graphs showing total monthly discharge of the Sacramento River and the 

south-bay streams and sewage effluent, and the corresponding changes 

in the surface salinity distribution in the south bay ---------------------------------- 6 

4. Vertical cross sections showing the salinity distribution along the longitudinal axis of the south bay in December 1969 and January 1970 ---------------------- 8 

5. Generalized surface salinity model for south San Francisco Bay ------------------------ 8 

6. Graphs showing comparison between the discharge of the large winter 

storms in wet and dry years and the corresponding distribution of 

surface salinities in the south bay-------------------------------------------------- 9 

7. Graph showing highest monthly average salinity for each year during 

1940-67 for two stations in the south bay and at the Golden Gate 

plotted against the total annual discharge for that year ------------------------------- 9 

8. Photograph showing the edge of the turbid low-salinity water that is 

carried into the south bay by the tide----------------------------------------------- 11 

9. Graph showing measurements of the salinity made in front of, and just 

behind, the edge of the low-salinity flow-------------------------------------------- 12 

10. Diagrammatic model of the salinity gradients and net surface and bottorn currents through the rna jor seasonal stages in the San Francisco 

Bay estuary --------------------------------------------------------------------- 12 

11. Map showing arrows drawn from release to recovery points of plastic 

markers that moved in near-bottom currents---------------------------------------- 14 

12. Graph showing seasonal salinity changes at three south-bay stations 

and the Sacramento River discharge------------------------------------------------ 16 

13. Graph showing seasonal distribution of phosphate in south San Francisco Bay----------------------------------------------------------------------- 16 

14. Graphs showing seasonal phosphate changes at three south-bay stations, the Sacramento River discharge, and the amount of phosphate 

contributed each month to the south bay from the San Jose city 

sewageplant--------------------------------------------------------------------- 19 

15. Graph showing comparison between the monthly discharge of the 

S~crarnento River at Sacramento from January 1969 to January 1970 

and the average and the range of monthly discharge of the Sacramento River at Sacramento from 1950 to 1967--------------------------------------- 19 

VII 

A PRELIMINARY STUDY OF THE EFFECTS OF WATER CIRCULATION 

IN THE SAN FRANCISCO BAY ESTUARY 

Some Effects of Fresh-water Inflow on the Flushing 

of South San Francisco Bay: 

A Preliminary Report 

By D. S. McCulloch, D. H. Peterson, P. R. Carlson, and 

T. J. Conomos 

INTRODUCTION 

The San Francisco Bay estuary (fig. 1) is used by the millions 

of people who inhabit its shore for municipal and industrial sewage 

disposal, recreation, commerce, fishing, and as a source of aesthetic 

pleasure. In large measure such uses depend upon the chemical character 

or quality of water. For many of these uses, the quality depends upon 

the balance between the rate with which chemical constituents are 

added to the estuary and the rate at which they are removed. 

The purpose of this report is to make data available to those 

interested in optimum development of the San Francisco Bay· estuary. 

A clear understanding of this estuary system is necessary for evaluating 

such things as the ability of the estuary to assimilate agricultural, 

municipal, and industrial waste products; the relation between the 

amount of freshwater inflow and the quality of the bay water; and 

the movement of water masses and entrained material within the estua~. 

In geometrically simple estuaries, unlike the San Francisco Bay, 

freshwater enters the estuary from one end and ocean water from the 

other. These waters are mixed by several processes within the 

estuary, principally by tides, and because the river discharge produces 

a ne~ outflow of these tidally mixed waters, the estuary is flushed.! 

The south bay (as used here, the bay south of the San Francisco-Oakland 

Bay Bridge) does not enjoy this normal flushing pattern, for there is 

no large freshwater discharge at its head near San Jose. Instead, the 

south bay is dependent upon water that enters it from the rest of the 

estuary system for its flushing.2 

Note--Numbered references in text are keyed to numbered items in appendix 

at end of chapter A. 

Al 
0 5 10 15 20 Miles 

SAN JOSE 

Figure 1.--Index map of the San Francisco Bay estuary showing locations of water sampling stations. 

A2 
The freshwater discharge of the Sacramento River is the major control 

of the salinity of San Francisco Bay north of the Oakland Bay Bridge.3 

Our analysis of available data indicates that the Sacramento River discharge 

also controls the seasonal variation in salinity of the south bay.4 

During years of high rainfall when the Sacramento River discharge 

is high (unless otherwise noted, "Sacramento River discharge" as used 

in this text, means the combined waters of rivers discharging into the 

Sacramento-San Joaquin deltaS), flushing significantly removes undesirable constituents from the south bay, but in low rainfall years (low 

Sacramento River discharge) the concentration of pollutants increases, 

sometimes reaching deleterious levels.6 This relation between the 

degree of flushing of the south bay and the Sacramento River discharge 

is qualitatively described in this report,7 This description is based 

on preliminary results of our study of short and long-term variations 

in physical and chemical properties of the water at 36 reoccupied 

stations in the estuary (fig. 1) and the adjacent Pacific Ocean.B The 

most useful of these properties are the salinity and the phosphate 

concentration. 

SALINITY9 

The salinity of San Francisco Bay as a whole is affected by the 

amount and the salinity of the Pacific Ocean water that enters through 

the Golden Gate, the amount of water that is discharge into the 

bay from streams, rivers and sewage outfalls, and by evaporation. The 

salinity of the bay responds to both seasonal and yearly changes in 

these factors. 

The dilution of Pacific Ocean water entering the Golden Gate by 

freshwater discharged into the bay largely controls the salinity of 

the bay water. For example, the mean monthly surface salinity values 

at three bay stations are shown for a 5 year period on Figure 2. One 

of these stations (Fort Point) is at the Golden Gate; the other two 

are in the south bay. Salinities at these three stations ranged from 

13 o/oo to 33 o/oo (parts per thousand by weight) throughout this 

period. This range is considerably larger • and the salinities considerably lower, than the annual range of 32.9 o/oo to 33.8 o/oo of the 

monthly mean salinity in the adjacent Pacific Ocean,lO Only during 

the period of low freshwater discharge in dry years does the surface 

salinity of the south bay approach or exceed Pacific Ocean salinity. 

Evaporation removes a layer of water approximately four feet in 

thickness each year from the bay.ll If water in the south bay was not 

exchanged, the salinity would increase by approximately 25%. Because 

the south bay water is almost always diluted by lower salinity water, 

the effect of evaporation is considerably reduced. However, as will 

be discussed later, evaporation can have a marked effect on seasonal 

salinity variation when the evaporation rate is high during the dry 

period of low freshwater discharge years. 

The discharge of south bay streams and sewage appears to have little 

effect on the salinity of the south bay. A comparison of total monthly 

discharge of the Sacramento River and the south bay streams is shown on 

Figure 2. Included in the south bay discharge is the maximum potential 

discharge of the existing south bay sewage facilities--which at times is 

A3 
.....-..._ 

+-' 

<1> 

<1> 

-I 

<1> 

L 

u 

0 

-0 

(/) 

c 

0 

E 

<1> 

(J) 

L 

0 

..r::: 

u 

(/) 

0 

~ 

..r::: 

+-' 

c 

0 

L 

0 ~--~-------------------------------------------------------~ 

~-~Soulliba~treams~~---~---

2 

3 

4 

5 

6 

7 

Jan. '51 

sewage effluent 

Sacramento 

'\.River 

(\____ 

SALINITY 

Fort Point--

Hunters Point------

A I am ed a ------------

/" 

I//'' 

"'-.)( 

I 

I 

Jan. '52 Jan. '53 Jan.' 54 Jan.' 55 Jan. '56 

Figure 2.-Comparison of the surface salinity changes at two stations in the south bay (Alameda and Hunters Point) and the 

Golden Gate (Fort Point) with the combined discharge of the 

Sacramento and San Joaquin Rivers and the combined discharge 

of the south bay streams and sewage effluent. 4 b, 5 , 12 

A4 

c 

0 

<1> 

- u oO 

(l) .. ~ 

OJ~ 

c u 

0 0 

LQ_ 

~+-' 

+-' c 

<l> 

c u 

0 

0 "'0 

lf) 0 

34 

32 

30 

28 

26 0 

0 

-

0 

24 ~ 

+-' 

22 c 

0 

lf) 

20 

18 

16 

14 

12 
much larger than south bay stream discharge.l2 The large difference 

in the discharge of these two river systems reflects the difference 

in the size of their drainage basins; the Sacramento - San Joaquin 

basin is approximately 45,420 square miles, as opposed to the drainage 

basins of the south bay streams that total approximately 1,850 square 

miles.l3 

Typically the Sacramento River has two periods of high discharge 

each year. The first occurs between December and February, and is 

rainfall runoff in the Sacramento - San Joaquin drainage basin, the 

second is caused by melting of the snow pack in the Sierras, is shorter 

in duration, and can occur any time from March through June.l4 South 

bay streams have a corresponding high winter rain runoff, but have no 

discharge peak corresponding to the snow melt. 

The variations in surface salinity at all stations shown in Figure 

2 reflect the Sacramento snow melt discharge that is absent from the 

south bay streams, even though Hunters Point and Alameda are in the south 

bay. Thus the south bay salinity is dependent in part on the Sacramento 

River discharge. In fact, the close correspondence of south bay 

salinity with major and even minor changes in the Sacramento discharge 

demonstrates a high degree of dependence throughout this entire period. 

A more detailed look at the salinity distribution of the entire 

south bay over a year's time shows the effect of the Sacramento River 

discharge more clearly. Throughout the year (January 1969-January 1970), 

salinity measurements were made on a nearly monthly basis at 36 stations 

in the bay. Sixteen of these stations are in the south bay (Fig. 1). 

Salinities were measured at the surface and throughout the water column.8 

The changing seasonal pattern of the surface salinity in the 

south bay for 1969 and part of 1970 is shown on Figure 3. On this 

figure, the stations are located along the vertical axis and time 

along the horizontal axis. Thus changes in salinity at a station can 

be read horizontally across the figure, and the changes in position of 

the salinity contours show the shift in the position of the salinity 

with time. In order to represent the salinity in terms of the volume 

of water, each station is plotted on the basis of the volume of water 

between it and the Oakland Bay Bridge, rather than the actual distance 

between the stations. This compensated for the narrowing of the south 

end of the bay.l5 

In periods of high Sacramento River winter rainfall discharge (top 

of Figure 3) low salinity water (less than 8 o/oo salinity, Jaunuary 1969) 

entered the south bay from the north. At the same time, or shortly after, 

the winter rainfall runoff in the south bay streams caused a local 

decrease in salinity at the south end of the bay (10.6 o/oo salinity, 

February 1969). This south-end decrease was extremely local and disappeared 

with the end of the south bay rainfall runoff. During the Sacramento snow melt 

discharge, that lasted until July, the south bay maintained a relatively 

low salinity (16 o/oo to 20 o/oo). Then as the Sacramento River discharge 

decreased the salinity increased, reaching a maximum (30 o/oo) in October. 

This pattern changed abruptly between December 1969 and Janu~ry 1970 when 

the Sacramento discharge increased rapidly, and low salinity water again 

entered the south bay from the north. 
"0 

c 

0 

(/) 

c 

0 

+-' 

0 

+-' 

(/) 

L 

Q) 

+-' 

:2 

+-' 

c 

0 

E 

+-' Q) 

2 

I 

Q) 

L 

u 

0 

0 

Ill 

c 

0 

E 

Q) 

rn 

L 

0 

.r: 

u 

Ill 

0 

0 +-' 

~ ~ 

c QJ -I Q) Q) 

~ ~ Q; 0 

.0 

0 L 

Q) (/) 

+-' c 0 0 

~ 

o E 

Q) 

E v ::J Ol 

0 "0 

> L 

m 

6~--------------------------------------------. 

I 

I I 

I I 

I I 

I I I 

I I I 

I I I 

I I I 

5 

4 

3 

2 

0.2 

0.4 

0.6 

0.8 

1.0 

1. 2 

----Sacramento River 

---- South bay streams and 

sewage effluent 

I 

I 

I 

I I 

I I 

I I 

I 

I I 

I I 

I I 

I I 

I I 

I I 

24-2 80/oo 8-12°/oo--1-+-<1-+ I 

12-160/oo 

Q) 1.6 +-' >. 0 0 E co X 

0 

L 

Q. 

Q. 

<( 

1.8 

Jan 

1969 

16- 200/oo 

Bay 

Bridge 

22 

(/) 

c 

0 

+-' 

0 

+-' 

V) 

figure 3.-The total monthly discharge of the Sacramento River 

and the south bay streams and sewage effluent 5 ' 12 upper, and 

the corresponding changes in the surface salinity distribution 

in the south bay, lower. The water-sampling stations are shown 

on the right in terms of the volume of water that lies between 

the station and the Oakland Bay Bridge. 15 

A6 
The salinity measurements taken at various depths at the 16 south 

bay stations allow us to examine the salinity distribution in vertical 

cross section before and after the rapid December to January salinity 

change (Fig. 4). 1b It is apparent from these profiles that the 

salinity of the entire south bay was profoundly changed. It is also 

clear from the January cross section that the low salinity water came 

from the north. 

The south bay seasonal salinity .changes described above can be 

represented diagrammatically by a three stage model (Fig. 5). In stage 

1 (December-February) the low salinity water produced by the high 

Sacramento rainfall runoff has entered the south bay, and has lowered 

the surface salinity at the north end. Following this initial discharge 

of the large winter storms, the low salinity water introduced from the 

north becomes mixed with the south bay wgter and reduces the salinity of 

the south bay. Following stage 1, the Sacramento River discharge 

decreases, resulting in ~ore saline water just north of the bay bridge. 

In stage 2 (March-May) this more saline water is introduced into the 

south bay, and raises the salinity at the north end of south bay. In 

stage 3 (June-November) the Sacramento and the south bay streams are at 

their lowest discharges. The average salinity of the south bay is at 

its highest value; the salinity may become highest in the center of 

the south bay due to evaporation and there may be a slight lowering of 

salinity at the north and south ends of the bay due to minor dilution. 

During periods of high Sacramento River discharge, then, water 

that enters the south bay from the north has a large effect on the 

salinity. Now one might ask, is it possible that the south bay 

dischbrge plays a more important role in controlling the south bay 

salinity when the Sacramento River discharge is low? Or rephrased, 

can local discharge into the south bay become important enough during 

low Sacramento discharge to reverse the salinity gradient proposed in 

the foregoing model? This question is largely answered in Figure 6, 

on which the discharge from the first major winter storms are compared 

to surface .salinities measured in the south bay. The size of the 

winter storms largely determines the wetness or dryness of the year. 

The salinity measurements indicate that salinities increased to the 

south in dry years as well as wet years. Thus the S cramento discharge 

is an important factor controlling the relative salinity distributicn 

of the south bay. This also indicates that stage 1 of the salinity 

model (Fig. 5) is valid for both wet and dry years. 

Although the decrease in Sacramento discharge in dry years does 

not change the relative salinity distribution of the south bay, it does 

have a strong effect on the absolute salinity values. This is clearly 

shown at Golden Gat~ Alameda and south of San Mateo on ~igure 7. On 

this figure the highest monthly mean salinity that developed during 

each year (for the period 1940-1967) is compared with the total discharge 

for that year. These data show that the lower the yearly river discharge, 

the higher will be the maximum salinity. It is importan~ to note, that 

in low discharge years, the salinity of the south bay can exceed that of 

the adjacent Pacific Ocean. This can only be achieved by evaporation 

which is, therefore, an important factor during low discharge years. 

A7 
0 

Q; 50 

<L> 

'+--

c 

L 

<L> 

-r' 

0 

3: 

Dec 19,1969 

0 

50 

Jan 2 7, 1970 

+ 5 10 +15 20 + 25 

Bay San Mateo Dumbarton 

Bridge Br1dge Bndge 

Distance from San Francisco-Oakland Bay Bndge (NautJcal M1les) 

Figure 4.--Vertical cross-sections showin~ the salinity distribution along the longitudinal axis of the south bay in December 1969 and January. 1970. 16 (These profiles have a vertical 

exaggeration of about X 580). 

:r 

J 

BAY 

South 

Stage 1 

Stage 2 

~ 

l 

Stage 3 

Figure 5.-Generalized surface salinity model for south San 

Francisco Bay. Stage 1 is the time of high Sacramento River 

discharge (Dec.-Feb.), stage 2 represents the period of decreasing discharge (March-Ma¥), and stage 3 is the period of 

low Sacramento River discharge (June-Nov.). 

AS 
5 10 25 

Bay Son ~--1ateo Dumbarton 

Br1dge Br1dge Br1dge 

Soc ramen to R1ver D1schorge D 1stance from San Fronc1sco Oakland Bay 

( cu feet /sec X 102) Br1dge lNout1col M1les) 

30 

25 

20 

0 

o'\ 

15 

0 

(/) 

Figure 6.--A comparison between the discharge of the large winter storms in wet and dry years and the corres~onding distribution of surface salinities in the south bay. ' 17 The size 

of the winter storms largely governs the wetness or dryness 

of the year. Thus, the small storm discharges at the top generally correspond to dry years, and the larger discharges at 

the bottom generally correspond to wet years • 

.. Approximate Locot1on 

• Golden Gate 36 • Alameda 

.. South of Son 

Mateo Bndge 

1'- 35 (() 

Ol 

0 

'I" 34 ~ 

~-.. \· - 33 • • 

?: .. • • c: 

• • ~ 32 • • c: • 0 • • •• .... Q) .... E • ...... • • • • 31 • • :.:::. • -·----·-- ~ 0 -- • • .... .. .... E 30 • • ' E • • .. ' :\ :::1 ,. • ·" X 

0 

2 29 

• .. 28 10 15 20 25 30 35 40 

Total annual Sacramento R1ver discharge 

(millions of acre-feet) 

Figure 7.--The h ghest monthly average salinity for each year 

during 1940-67 for two stations in the south bay and at the 

Golden Gate plctted against the total annual discharge for 

that year. 18 In wet years, the salinities are low, but in dry 

years, the salinity can equal or exceed the salinity of the 

adjacent ocean. 

389-708 0 - 70 - 2 A9 
These data are also relevant to flushing, and are reconsidered in a 

later discussion. 

Thus far we have described changes in salinity of the bay as 

related to changes in Sacramento discharge without considering the 

way in which the diseharge causes the salinity change. The following 

is a generalization of the estuarine circulation in San Francisco Bay. 

These processes areoomplicated and poorly known.l9 when Sacramento 

River water enters the bay it has a hydraulic head that enables it to 

flow down the estuary. Because of its lower salinity, the incoming 

river water is less dense than the water in the estuary, ~nd it flows 

on top of the more saline water. As the low salinity water moves seaward it is subjected to turbulence from tidal currents and winds that 

mix it with the underlying water. The tidal currents carry the water 

forward and backward along the estuary, but the surface water has a net 

movement toward the ocean due to the net effect of the hydraulic head, 

and to horizontal forces produced by the salinity (density) gradient 

within the surface water. At the same time there is net movement of 

the underlying more saline water back up the estuary beneath the low 

salinity surface water. For simplicity these net movements can be 

called net surface anQ net bottom currents. 20 

Of the above, the size of the discharge (i.e., the hydraulic head 

and the amount of freshwater available to dilute the water in the 

estuary) and the net surface and bottom currents are often important 

in determining salinity changes. Tidal action is also extremely important 

in transporting and mixing the w~ter within the bay, but it is relatively 

constant throughout the year. Thus, although tides affect the response 

time to changes in the freshwater inflow, they are not respon~ible for 

seasonal salinity variation. 21 V.Jind mixing can be important, 22 but at 

the scale of the gross changes we are considering, it can be neglected. 

Some feeling for the extent to which the tide can be effective in 

wixing low salinity water derived from the Sacramento River with water 

in the south bay can be obtained by following the edge of the tide as 

it flows south into the south bay. For about one half hour before the 

tide runs into the south bay low salinity water from San Pablo Bay, 

which is sometimes highly turbid, enters the north end of the south 

bay·. 23 w'hen the tide turns, this San Pablo Bay water is transported 

southward; the low salinity turbid water can be f~tlowed for at least 

ten miles sctuth of the Bay Bridge (Fifs. 8 and 9). 

The net surface and net bottom currents which may be presumed on 

the basis of the observed salinity distribution are st1own in a highly 

diagrammatic form on Figure 10. The three stages represented for the 

entire estuary are the same three stages outlined earlifr in the south 

bay salinity model (Fig. 5). Throughout all stages the net C"Qrrent 

pattern does not change in the central and northern bays. 

Because the south bay is an af:.~pendix-like feature of the estuary, 

lacking its own through-going drainage, its circulation is quite different from circulation in other parts of the estuary. Durin~ maximum 

Jacramento River discharge (stage 1, Fig. 10) the observed salinity 

distribution indicates that net bottom c~rrents flow toward the central 

bay. Tnis circulation pattern may last several months. These are 

AlO 
Figure 8.--A view looking north at the edge of ~he turbid low 

salinity water that is carried into the south bay by the 

tide. Note Hunters Point and San Francisco on the left, the 

Oakland Bay Bridge in the background and Alameda on the 

right. 

All 
10 

• 20 

~ 

"' 0. 

~ 30 

40 

• Low Sol1n1ty Water 

o South Bay Water 

soL-~-L~~--L-~-L~--L-~~~ 

8 10 12 14 16 18 20 

Figure 9.--Measurements of the salinity made in front of, and 

just behind, the edge of the low salinity flow. Note that the 

low salinity water is clearly distinct from the south bay wa -

ter to a depth of about 20 feet. 

Surface and bottom currents Salinity gradient 

Stage 1-Maxi mum Sacramento River discharge 

Duration approx. 1/4 year 

--

--

Stage 2- Decreasing Sacramento River discharge 

Durat1on approx. 1/4 year 

Stage 3- Low Sacramento River discharge 

Durat1on approx 1/2 year 

Figure 10.--A highly diagrammatic model of the salinity gradients and net surface and bottom currents through the major 

seasonal stages in the San Francisco Bay estuary. The curved 

lines on the right-hand figures indicate salinity contours; 

H indicates high and L indicate s low salinity. 

Al2 
probably the most rapid net currents in the south bay, for the strength 

of these net currents depends in part upon the size of the horizontal 

salinity differences present--which are greatest during this stage. 

As the Sacramento River discharge decreases (stage 2) the south bq 

salinity gradient reverses and the net surface and net bottom currents 

run in the opposite direction, and are of lower magnitude. This pattern 

may also last several months. Throughout the remainder of the year 

(stage 3), when there is almost no salinity gradient in the south bay, 

the net currents are probably extremely small and ineffective and their 

directions may var,y. 

The inferred pattern of net currents is supported for the central 

and northern bays by preliminary results of a study of the near-bottom 

currents.25 Weighted plastic markers designed to move with near-bottom 

water were released in San Francisco Bay and along the adjacent Pacific 

Coast. Arrows drawn from release points to recover,y locations show net 

bottom current movement from the Pacific Ocean and from the northern 

edge of the south bay into San Pablo Bay (Fig. 11). Recoveries from the 

south bay are so few that they are not a positive test of the proposed 

net current model. The movement of these markers not o~ demonstrates 

the existence of net bottom currents but also indicates the paths that 

will be followed b,y fluids or solids that are entrained in these currents. 

FLUSHING OF THE SOUTH BAY 

With the exception ~f salinity increases due to evaporation, changes 

in the seasonal salinity distribution described in the foregoing must 

result from the movement of salt into and out of the south bay. The 

magnitude of the changes, which indicate the volume of water exchanged, 

the time distribution of the salinity changes, and the net surface and 

bottom currents, can be combined to form a generalized picture of the 

seasonal and yearly flushing pattern of the south bay. 

For example, if one considers the year 1969-1970 shown in Figures 

3 and 4, a large and abrupt salinity change o•curred between December 

and January. During this interval the average salinity of' the south 

bay decreased tram approximately 26.5 o/oo to approximatelY 14 o/oo. 26 

This salinity change can be used to estimate how much flushing occurred. 

The lower the salinity of the flushing water, the less need be introduced 

to produce the observed salinity change. To take an extreme: if the 

salinit:y of the flushing water is 0 o/oo, then 47% of the vollllle of the 

south ba:y would have to have been replaced (i.e., 1,034,000 out or 

2,200,000 acre feet). The only sources of water that approach 0 o/oo 

salinity in the south bay are the local streams and the sewage. But 

their combined maximum annual discharge (165,570 acre feet) is onlY 7.5% 

of the volume of the south bay. Comparison with the amount of water 

needed to flush the south bay reemphasizes the ineffectiveness of the 

south bay stream and sewage discharge in determining aouth bay salinity. 

A more realistic estimate of the minimum amount of water that must 

be flushed fran the south bay to achieve the December to January salinity 

change can be made by assuming that the flushing water had a salinity 

equal to the lowest salinity measured in the south bay. This was 5. 3 

o/oo, measured in Januar,y 1970, at the Oakland Bay Bridge in the southward flowing San Pablo Bay water described aboTe. Flushing water of 

A13 
Figure 11.--Arrows drawn from release to recovery points of 

plastic markers that moved in near-bottom currents. 25 Markers 

were released on March 5 and 6, 1970, and the arrows shown 

are those that were recovered by April 22, 1970. These arrows 

indicate the direction of the net bottom currents. 

M4 
this salinity would require that approx:i.Dlately 59% of the volume of 

the south bay be replaced. The actual amomt of water removed must 

have been larger, not onlY because the average salinity of the replacing 

water was certainly greater than 5.3 o/oo, but also because same mixing 

of the south bay and flushing water BlUSt have occurred during the 

exchange. 

This method of approximating the amount of flushing cannot be 

applied as reliably for the balance of the year because south bay and 

flushing water cannot be clearly differentiated when their salinities 

approach one another.27 However, the seasonal :;alinity variations in 

the south b~ closely parallel the changes in Sacramento River discharge 

throughout the year. This is shown on Figure 12, on which the Sacramento 

River discharge is plotted with discharge increasing downward. Also 

shown are three curves or the yearly changes in salinity measured at 

Hunters Point (sta. 23), San Mateo Bridge (sta. 25) and Redwood Creek 

( sta. 30). The general agreement between the salini t~ changes and the 

Sacramento discharge emphasizes their close relation. 

In the foregoing we have discussed salinity_changes over a single 

year. The salinity distribution can also be related in a generalized 

way to changes in the total annual discharge for the period 1940-1967 

shown earlier in Figure 7. In this t,igure, lines drawn through the 

highest salinity values at south bay locations show that them was an 

accelerated decrease of salinity with high annual discharge, and an 

accelerated increase during years of low annual ~scharge. Part of the 

accelerated salinity increase in dey years was due to evaporation, but 

the effects of evaporation (which goes on in wet, as well as 'dry years) 

can become important in increasing salinity only if there is a reduction 

in the amount of water exchanged in the south b~. 

PHOSPHATE29 

Like salinity, the annual change in phosphate in the south bq 

water shows an inverse relation with the Sacramento River discharge. 

That is, when discharge increases, phosphate decreases, and vice versa. 

However, phosphate differs from salinity in two important ways. (1) Salt 

is introduced from the north, whereas phosphate is introduced into the 

south bay primarily in sewage effluent discharged into the south bay. 

(2) Salinity is conservative, that is, its concentration is detennined 

primarily by mi.Xiiig and current transportation, whereas phosphate ismnconservative, and ita concentration is further controlled b,y biologie&r and 

geocheiicil processes. Therefore, the accumulation ot phosphate indicates 

that the supp~ exceeds removal, and the removal indicates the net effect of 

flushing and consumptive processes. 

The annual phosphate distribution (Fig. 13) indicates a dominant 30 

source of phosphate at the aouth end of the south bay (San Jose sewage). 

Sewage from the other major dischargers (San Francisco and Oakland) 

located near the north edge of the south bay, apparent~ is dispersed 

northward from the south bay. 

The annual variation in phosphate parallels tbe annual salinity 

variation (compare Figure 3). Salinity and phosphate levels are low in 

late spring, then both climb, reaching peak concentrations late in the 

year. Then the salinity and phosphate concentrations undergo a rapid 

A15 
30 

25 

0 

0 

0 

>. 20 .!:: 

c 

c 

If) 

15 

r---------------------------------------------------~0 

--- --- Sta. 23 

Sta. 25 

Sta. 30 

I 

I 

I 

I , 

, , ----\ 1// Sacramento I 

April 

1969 

M J J 

Rrver drscharge 

A s 0 N D Jan. 

1970 

.., 2 m 

'-

c 

s::. 

u 0 VI E u ... 

3 t I 

> v ·a: b 

B 

4 ~ 

E 

c 

'-u 

c 

If) 

c 

VI 

c 

0 

E 

... 

l .0 ~ c 

s::. s::. ...... :J 

v 0 OlVI 

L. 

~0 

u 0 

~ ~ 

uo <.D c 

- u 

~ ~ L. 

c 0 tJ 

~~d U L 3 

Figure 12.--Seasonal salinity changes at three south bay stations, and the Sacramento River discharge (the latter is shown 

with discharge increasing downward). Note the general correspondence between the changes in salinity and the discharge. 

u 

c 

0 

Ill 

c 

Q 

... 

2 

Ill 

c 

IV 

IV 

~ IV 

.0 

L 

2 

0 

3 

~ Q) 

Q) 

i 

ell 

'-

u 

a 

0 

If) 

c 

0 

-

E 

0 Q) 

Ol IV U 

~ l: 

a co > >. 

2 ~ a 

E 

X 

0 

L. 

Cl 

Cl 

<( 

0.2 

0.4 

06 

08 

10 

12 

14 

1.6 

1.8 

-10-;.cg -at. P/L as P04 

(0. 95) ppm PO" 

~~~--~------------~~--, 2~Bay Bndge 

If) 

c 

Q 

... 

a 

... 

\/) 

San Mateo 

Br1dge 

Figure 13.--Seasonal distribution of phosphate (in microgram 

atoms of phosphorus per liter as phosphate and parts per million phosphate) in south San Francisco Bay. As in figure 3, the 

stations are located on the basis of the volume of water that 

lies between the station and the Oakland Bay Bridge. 

Al6 
decrease during the major increase in Sacramento River discharge between 

late December and January. 

The amount of flushing that occurred bet·ween December and January 

can be estimated from the change in phosphate concentration as it was 

for the change in salinity. 31, 32 Using the lowest phosphate value 

measured in January in the south bay (2.6 micro gram atoms/liter) as 

the phosphate concentration of the flushing water, the amount required 

to produce the observed change in the south bay concentration from the 

December average of 11.0 to the January average of 6.3 ~g.-at./1 would 

mean that 56% of the volume of the south bay water was replaced. This 

agrees with the 59.% flushing volume computed from the salinity. Because 

phosphate is not strictly conservative, better agreement between the 

flushing volumes computed from the phosphate and salinity data would be 

fortuitous. 

Before interpreting the changes in phosphate levels throughout the 

year in terms of flushing, two factors must be considered: (1) when and 

how much phosphate was removed by biologic and nonbiologic agents, and 

(2) when and how much phosphate was supplied to the south bay? 

The removal of phosphates to bottom sediments is not evaluated in 

this report. The seasonal loss of sediment-associated phosphate that 

accumulates on the bottom of the south bay is not known. The rate of 

organic growth (phytoplankton) can produce significant changes in 

phosphate concentration that must be considered. In general phytoplankton growth increases during one or more blooms of weeks in duration, 

in the period of high duration and intensity of sunlight. This can be 

followed by a rapid decrease in phytoplankton growth. There has been som33 study of phytoplankton growth in the northern part of San Francisco Bay, 

but little is known about the magnitude or the time at which blooms occur in 

the south bay. 

The amount of phosphate supplied to the south bay is difficult to 

estimate. The only measurements of phosphate in sew~ge effluent avail~ 

able to the authors are from the city of San Jose. 34 If, as it appears, 

San Francisco and Oakland contribute little sewage that remains in the 

south bay, then San Jose sewage is quantitatively important. The city 

of San Jose contributes approximately 40% of the balance of the sewage 

discharged into the south bay.30 The monthly amount of phosphate in 

San Jose sewage is shown on Figure 14 along with changes in phosphate 

measured at Hunters Point (sta. 23), San Mateo Bridge (sta. 25) and 

Redwood Creek (sta. 30). The higher phosphate concentration at the 

southern stations reflects the southern source. 

The cumulative curve of the phosphate supplied to the south bay 

(Fig. 14) indicates that if the south bay was not flushed and phosphate 

was not removed by biological consumption and sedimentation, phosphate 

would increase. Thus the observed decrease in phosphate concentration 

that coincides with the high runoff period indicates rates of flushing 

and biologic and nonbiologic removal in excess of rates of supply. Therefore, the change in phosphate concentration, as well as the change in 

salinity is related to the changes in Sacramento River discharge. 

The change in the Sacramento River discharge parallels the change 

in phosphate concentration at Redwood Creek (sta. 30). The 

Al7 
relation of the discharge to the phosphate concentration at Station 

30 suggests that flushing exerts a considerable influence on the amount 

of phosphate in the south bay regardless of biologic and nonbiologic 

removal of phosphate. Because this station 30 is well at the south end 

of the south bay on a volume basis, it appears that the Sacramento River 

discharge has a large effect over the entire south bay. 

Flushing by Sacramento River inflm-t and consu.mption by phytoplankton 

may effectively remove the phosphate dissolved in south bay waters. In 

the winter and spring, flushing increases, whereas in the late spring 

and sum~er, biological cons~~ption probably increases. Both the steady 

increase in phosphate concentration from April to July, and the major 

winter decrease, strongly indicate that phosphate removal is primarily 

a consequence of flushing. 

As shown on Figure 14 the phosphate concentration does· not change 

greatly between.late July and early December. In 1969, when the 

Sacramento River discharge ~ was at about one million acre feet per month 

from July through November, phosphate remajned relatively constant 

indicating that phosphate was being removed as rapidly as it "tvas being 

supplied·. The summer discharge was hi.o-her in 1969 than the average for 

the years 1950 tr~ough 1967 (Fig. 15).J5 If Sacramento River discharge 

contributes significantly to flushing o.f the south bay at these low flow 

levels, then in years with average. runoff the phospha·l:.e concentration may 

be higher in the sout~ bay. 

Our data show that the surnmer accu..'llulation and subsequent winter 

removal of phosphate in the south bay is highly suggestive of a seasonal 

modulation of the flushing rate. There is no evidence for a corresponding 

seasonal modulation of the tides .36 However, the correspondence bet-"'reen 

the seasonal variation in the observed phosphate concentrations and 

changes in the Sacramento River discharge argues for a cause and effect 

relation bet-vmen river discharge and flushing. 

SUHM.ARY 

(1) The seasonal salinity variation of the south bay is largely 

controlled by fresh water from the Sacramento River under present conditions 

and is nearly unaffected by the comparatively minor discharge of south 

bay streams and sewage. 

(2) The observed seasonal change in the phosphate concentration in 

the south bay does not appear to be explained.by tidal flushing. The 

change in phosphate concentration does, hm-tever, correspond with the 

seasonal change in the Sacramento River discharge. Appar~ntly changes 

in net flow of fresh water to the bay from this source is an important 

controlling factor in flushing of the south bay. 

(3) The indicated relation between the Sac~amento River discharge 

and flushing suggests that soluble waste materials are removed from 

south bay largely during periods of high river discharge. • 

(4) Investigations nm.v in progress should further refine this 

qualitative description of the flushing of south San Francisco Bay and 

the seasonal salinity and circulation pattern in the estuary. 

AlB 
tJ 

CTI 

L. 

c 

.s::: 

u 

Ill 

·-u 

L. 

tJ 

> 

a: 

E 

c 

tJ 

E 

c 

L. 

u 

c 

1/) 

Figure 14.--Upper, Seasonal phosphate changes at three south bay 

stations and the Sacramento River discharge (the latter is 

plotted with discharge increasing downward). Lower, The amount 

of phosphate (metric tons) contributed each month (shown as the 

monthly and the cumulative amount) to the south bay from the 

San Jose city sewage plant. ~ 

r-----------------------------------------------------------------~80 

Sacramento R1ver diSCharge (at Sacramento) 1950-1967 

Rang{ t Average 

4 

0 

60 

E 

:; 3 

i 

tJ 

L. 

u 

~ Dos,harge Jan. 1969-Jan 1970 

40 c 

Ill 

c 2 0 

E 

20 

0 ~----------------------------------------------------------------~ 0 

J F M A M J J A s 0 N 0 J 

Figure 15 .--A compa·rison between the monthly discharge of the 

Sacramento River (at Sacramento) from January 1969 to January 

1970 and the average and the range of monthly discharge of the 

Sacramento River (at Sacramento) from 1950 to 1967. Note that 

July through October was wetter than the average and even higher than the previous August range. 

Al9 

tJ 

CTI 

L. 

.s::: 

c ~ tJ u 

Ill ~ "'0 ~ 

L. u v ·.a > ·a: :I 

u 

~ Ill 

"'0 

c c v c 

E Ill 

:I c 0 L. 

u ~ c 

1/) 
APPENDIX 

1. As used in this report, the term flushing refers to the removal of a 

parcel of water, with its contained constituents, from a given 

area. 

2. The San Francisco Bay estuary has received considerable study. See for 

example: 

(a) Selleck, R. E., Pearson, E. A., Glenne, Bard, and Storrs, 

p. N., 1966, Physical and hydrological characteristics of 

San Francisco Ba:;··, v. 4 of A comprehensive study of San 

Francisco Bay--Final report: Sanitary Eng. Research I.a.b., 

California Univ., Berkeley, SERL Rept. 65-10. 

(b) McCarty, J. c., and Harris, H. s., 1967, The future of an 

estuary: Natl. Symposium on Estuarine Pollution, Stanford 

Univ., Stanford, Calif., 1967, Proc., p. 335-369. 

(c) Federal Water Pollution Control Administration, 1967, Effects 

of the San Joaquin Master Drain on water quality of the San 

Francisco Bay and Delta: Central Pacific Basins Comprehensive 

Water Pollution Control Proj. rept. 

(d) Kaiser Engineers, 1969, San Francisco Bay-Delta water quality 

control program--Final report (prelim. ed.) to the State of 

California, 360 p., plus app. 

3. Roden, G. I., 1967, On river discharge into the northeastern Pacific 

Ocean and the Bering Sea: Jour. Geophys. Research, v. 72, no. 22, 

p. 5613-5629. Also see page 89 of article cited in 2 (a) above. 

4. Sources of salinity data: 

(a) 1912-1913. Summer, F. G., Louderback, G. D., Schmitt, w. c., 

and Johnston, E. c., 1941, A report upon the physical conditions in San Francisco Bay, based upon the operations of 

the United States Fisheries Steamer "Albatross" during the 

years 1912 and 1913: California Univ. Pubs. Zoology, v. 14, 

no. 1; 198 p. 

(b) 1921-70. u.s. Coast and Geodetic Survey, unpublished data 

for: Fort Point· (1921-present), Hunters Points (1945-6 and 

1951-56), and Alameda (1939-present). 

A20 
(c) 1963-4. Storrs, P. N., Selleck, R. E., and Pearson, E. A., 

1965, Appendices to a comprehensive study of San Francisco 

Bay 1963-1964: Fourth Annual Report SERL Rept. No. 65-2, 

Univ. Calif., Berkeley, p. B-38-9. 

(d) 1963-5-6. Aplin, J. A., 1967, Biological survey of San 

Francisco Bay, 1963-1966: California Dept. Fish and Game, 

Marine Resources Operations Lab. rept. 67-4. 

(e) 1969-70. Measurements by the u.s. Geological Survey, using 

an electrodeless induction salinometer. 

5. The discharge given as Sacramento discharge includes the discharge of 

the major tributaries to the bay in the Sacramento and San Joaquin 

basins. Discharges were measured at u.s. Geological Survey gaging 

stations on the Sacramento River at Sacramento, San Joaquin River 

at Vernalis, Mokelumne River at Woodbridge, Cosumnes River at 

McConnell, Calaveras River at Jenny Lind, Dr.y Creek at Galt. 

6. It 

No measurements were made of actual discharge from the Delta to the Bay 

because of technical difficulties involved in determining the fresh 

water component of two-phase flow in tidal reaches. (see: Smith, 

Winchell, 1969, Feasibility study of the use of the acoustic velocity meter for measurement of net outflow from the SacramentoSan Joaquin delta in California: u.s. Geol. Survey Water-Supply 

Paper 1877, 54 p.) Despite the lack of an exact measure of the 

discharge from the Delta, the fresh water flow data are considered 

to be sufficiently representative for the qualitative discussions 

in this report. 

South bay discharge includes Colma Creek, Redwood Creek, San Francisquito Creek, Matadero Creek, saratoga Creek, Guadalupe River, 

Patterson Creek (Alameda), San Lorenzo Creek. 

The Southern Estuary now exhibits the most serious reduction of 

benthic animal diversity due to toxicity and the highest levels 

of nutrients. Both phenomena are associated at least in part with 

an insufficiency of tidal exchange and flushing flows to dilute 

the municipal and industrial effluents now discharged to the area. 

The Northern Reach receives sufficient inflow from the Delta in 

conjunction with dilution from tidal exchange to dilute waste effluents discharged to that area ••• " Biologic Ecologic Study, 1968, 

State of Calif. State Water Quality Control Board, Final Report, 

Task VII-Ib, p. v-9· 

7. The relation between Sacramento River discharge and the salinity of the 

south bay was pointed out in Peterson, D. H., and Carlson, Paul, 

1968, Influence of runoff onseasonal changes in salinity 

~1 
in San Francisco Bay, California [abs,]: Am. Geophys. Union Trans., 

v. 49, p. 704. 

8, Since 1968, the Office of Marine Geology and the Water Resources Division 

of the u.s. Geological Survey have carried on an investigation of 

the geology and coastal hydrology of San Francisco Bay. Study has 

been directed toward 1) the bedrock basin and overlying sediments 

and 2) the modern depositional environment. The principal aim of 

the latter is to understand the relation between the chemistry and 

circulation of the bay water, and the origin, transportation, and 

deposition of the suspended and bottom sediments, Monthly sampling 

at reoccupied stations since January 1969, has included: 1) Salinity, conductivity, temperature, turbidity (percent light transmission), All measured throughout the water column. 2) Water samples 

(2 meter depth) examined for suspended particles, silicate, phosphate, nitrate, nitrite, dissolved and particulate carbon, 

9, Salinity is the total amount of dissolved material in grams contained in 

one kilogram of seawater, Our salinity measurements were made with 

a field salinometer with an accuracy of about 1 part per thousand. 

10, Lynn, R. J., 1967, Seasonal variation of temperature and salinity at 10 

meters in the California Current: Calif. Coop, Fisheries Invest. 

Reports, v. 11, p. 157-174. 

11. Evaporation increases steadily from a low (1.3 in) in January, to a high 

(7.3 in) in July, then decreases to a low (1,3 in) in December, The 

total (mean annual) evaporation is 47.8 in. (Reference cited in 

2a). 

12, The maximum potential sewage discharge of the existing south bay sewage 

treatment plants is approximately 60,000 acre feet per month. (San 

Francisco Bay Conservation and Development Commission, 1967, Water 

pollution and San Francisco Bay: San Francisco Bay Conser. and 

Devel. Comm. rept. 

13. Porterfield, G., Hawley, N, L., and Dunnam, c. A., 1961, Fluvial sediments transported by streams tributary to San Francisco Bay area: 

u.s. Geol. Survey, (Rept. prepared for u.s. Army Corps of Engineers, 

San Francisco Dist.). 

14, The discharge is highly regulated by water management facilities, but the 

peak discharges controlled by these facilities that do enter the bay 

are related to the winter rainfall and later snowmelt, 

15. The volume of the water between any station and the Oakland Bay Bridge 

was approximated from the volume distribution given in the reference 

cited in 2a above. 

16. Salinity o/oo Dec. 19, 1969, and Jan. 27, 1970. 

~2 
Feet Depth (feet) 

below 

Station surface 8 16 24 32 36 40 48 60 

Salinity o/oo Dec. 19, 1969 

21 27.1 27.2 27.2 27.2 27.2 27.2 27.3 

23 27.1 27.1 27.2 27.3 27.4 27.5 

26 27.2 27.3 27.4 27.5 2'7.6 

28 26.8 26.9 26.9 27.0 27.1 

30 26.8 26.8 26.7 26.7 26.8 26.8 26.9 

32 25.2 25.3 25.6 26.1 

34 25.1 25.2 26.0 

36 24.5 24.5 24.7 25.0 

Salinity o/oo Jan. 27, 1970 

21 5.3 5.3 5.7 12.3 14.0 25.0 

22 5.3 6.0 7.9 10.6 

23 6.9 7.0 7.8 8.0 9.1 16.3 17.1 

24 9.2 8.8 10.3 13.0 19.5 

24a 10.4 10.3 10.7 14.0 19.0 

25 9.6 10.5 10.5 13.0 16.2 

26 10.6 10.6 12.0 14.0 16.3 16.4 

28 12.5 12.5 12.6 14.0 16.4 16.5 

29 12.7 12.7 12.8 14.8 16.5 -16.7 

30 13.5 13.5 13.5 15.0 15.8 16.6 16.8 

31 14.9 14.9 15.0 16.2 16.5 16.5 

32 15.5 15.5 15.8 16.2 16.6 

34 16.6 16.6 16.6 

35 16.0 16.0 16.1 16.2 16.3 

36 15.6 15.6 15.7 

A23 
17. The Sacramento River discharge used is the average discharge for the 

three weeks preceeding the time at which the salinity was measured. 

18. Data from 1) Sanitary Engineering Research Laboratory; University of 

California, Berkeley, Assorted publications, 1958-64, and 2) u.s. 

Coast and Geodetic Survey: unpublished data. 

19. The general character of circulation patterns vary between estuaries and 

quite often vary within estuaries, both spatially and seasonally. 

The basic factors in determining the type of circulation are (1) the 

relative interactions and magnitudes of the river discharge and the 

tidal currents, (2) the physical dimensions of the estuary, and 

(3) the effect of the earth's rotation (Coriolis force). Two general descriptions of physical processes of estuarine circulation are 

by Bowden, K. F., 1967, Circulation and diffusion, p. 15-36 !a Lauff, 

G. H.,ed., Estuaries: Am. Assoc. Adv. Sci. Pub. 83. 

Pritchard, D. w., 1967, Observations of circulation in coastal plain 

estuaries, p. 37-44 £a Lauff, G. H.,ed., Estuaries: Am. Assoc. Adv. 

Sci. Pub. 83. 

20. These are broad inferences to the nature of the circulation from salinity 

determinations and comparison to other estuarine systems; long term 

current measurements will be needed to evaluate the net current 

velocities. 

21. " ••• Tidal currents, which alone do not result in any net transport of 

water over a complete tidal period, exert a profound influence 

through the turbulent mixing they produce. This tends to break 

down the interface between the river water and salt water and produce a mixing of the two waters ••• " Bowden, K. F., p. 16, cited 

in 19 above. 

22. " ••• It ~s apparent that the wind can have an important influence onestuarine circulation and mixing. Through the stress exerted on the 

surface it can produce a net transport of water, and the waves generated will increase the intensity of vertical mixing. In the surface layer the water transport will be mainly in the direction of 

the wind, so that the normal seaward flow will be increased if the 

wind is blowing down-estuary; it will be decreased, or even reversed in direction, if the wind is up-estuary. Compensating currents occur which influence the flow in the deeper layer also. The 

increased mixing because of wind currents and waves may have an important effect on the salinity structure, causing a breakdown in 

the normal pattern of stratification ••• " from Bowden, K. F., p. 34-

35 cited in 19 above. 

23. Smith, B. J., 1966, The tides of San Francisco Bay: San Francisco Bay 

Conserv. and Devel. Comm. rept. 
24. Rhodamine dye was air-dripped at five places within this water 

mass about 1000 feet behind its advancing edge. The dye 

spots were rapidly elongated parallel to the direction of 

~ovement of the flow (i.e., perpendicular to the edge). 

Thus the water is moving faster and accelerating toward 

its advancing edge. It must then roll under as the plume 

overrides south bay water. 

25. Chapter B of this report. 

26. The average salinity was calculated from the cross section shown 

on figure 4, and the data were weighted for the volume of 

water between the measuring stations and the Oakland Bay 

Bridge (see 2a above). 

27. Any dissolved constituent that can be considered to be conservative can be used to estimate the volumes of two different 

water types in a mixture if the concentration of the 

constituent is significantly different in the two water types. 

28. The Sacramento River discharge is superimposed on the salinity 

curve in such a way as to make the observed change in 

salinity that occurred before December and January coincide 

with the change in Sacramento discharge for the same period. 

The discharge curve is drawn from the data given in figure 

3, with the exception that the December discharge is r~duced 

by interpolation to account for the fact that most of the 

discharge increase in December occurred after the sampling 

cruise. 

29. Phosphate samples were collected as in 8 above. The concentration 

of hydrolyzable and orthophosphate in the samples was determinated by an automated adaptation of the Fiske and Subbarrow 

procedure using 1-amino-2-naphthol-4-sulfonic acid (ANSA) as a 

reducing agent for phosphomolybdic acid. 'Inorganic Phosphate', 

Technicon Laboratory l~thod File N-4b, Technicon, Inc., 1965. 

(Technicon Controls Inc., Chauncey, N.Y.). 

30. A 1967 spot check by the BCDC (Hater Pollution and San Francisco 

Bay) of sewage discharge into the south bay showed that the 

San Jose discharge (62 million gallons per day) was 38% of 

the total daily discharge (163.3 mgd) excluding the discharge 

from Oakland and the southeastern San Francisco plant. Of 

this 163.3 mgd, 86% (140 mgd) was discharged south of the 

San Mateo Bridge. 

389-708 0 - 70 - 3 

A25 
31. A nonconservative element can be used to indicate flushing when 

the amount of change in the concentration of the element 

can be shown to greatq exceed the expected amount of removal 

by biological consumption. Assuming an average depth of 6 

meters, and using a commonly accepted ratio of carbon to 

phosphorous utilization of 106:1 by atoms (Redfield, Ketchum, 

and Richards, 1963) the change in phosphate from December to 

January would require 120 grruns of carbon per square meter 

per day. Such a rate of phosphatic utilization of carbon is 

10 to 100 fold greater than the highest expected rates in 

the most fertil natural environn1ents (Ryther, 1963). Thus 

the large change in phosphate between December and January 

must be largely due to flushing. 

(a) Redfield, A. c., Ketchum, B. H. and Richards, F. A., 

1963, The influence of organisms on the composition of sea 

water, p. 26-77 in Hill, M. N., ed., The Sea: Vol. 2, John 

Wiley and Sons, New York. 

(b) Ryther, J. H., 1963, Geographic variations in productivity, 

P• 347-380 in Hill, M. N., ed., The Sea: Vol. 2, John Wiley 

and Sons, New York. 

32. The phosphate concentration measured at two meters was taken as 

representative of the water column at the station. Average 

phosphate for the entire south bay was then calculated 

weighting each station for the volume of water between it 

and the Oakland Bay Bridge (see 2 above). 

33. See for example: 

(a) Bain, R. c., and HeGarty, J. c., 1965, Nutrient productivity studies in San Francisco Bay: u.s. Public Health 

Service, Central Pacific Basins Water Pollution Control 

Proj. Tech. Rept. 65-1. 

(b) Peterson, D. H., Carlson, P. R., and McCulloch, D. s., 

1970, Photosynthetic utilization of dissolved silica 

and production of suspended particles, San Francisco 

Bay estuary /abs.7: EOS (Am. Geophys. Union Trans.), 

v. 51, no. 4~ p.-318. 

34. Phosphate data (effluent total phosphorus) courtesy of Mr. Harr,y 

Sanders, senior chemist, San Jose, Santa Clara Sewage treatment plant. Honthly discharge data are from unpublished 

monthly report from the same source. 

A26 
35. On this figure, the discharge of the Sacramento River is as 

measured at Sacramento. 

36. u.s. Coast and Geodetic Survey, 1969, Tidal current tables, 

Pacific Coast of North America and Asia, 254 p. 

u.s. Coast and Geodetic Survey, 1969, Tide tables, West Coast 

of North and South America, 224 P• 

A27 

Movement of Seabed Drifters in 

the San Francisco Bay Estuary 

and the Adiacent Pacific Ocean: 

A Preliminary Report 

By T. J. Conomos, D. H. Peterson, P. R. Carlson, and D. S. McCulloch 

A PRELIMINARY STUDY OF THE EFFECTS OF WATER CIRCULATION 

IN THE SAN FRANCISCO BAY ESTUARY 

GEOLOGICAL SURVEY CIRCULAR 637-B 

Prepared in cooperation with the 

U.S. Department of Housing and 

Urban Development 

CONTENTS 

Introduction--------------------------------------------------

~ethods----------------------------------------------------­

Results------------------------------------------------------

[ijscussion---------------------------------------------------

Appendix ----------------------------------------------------

ILLUSTRATIONS 

Page 

81 

1 

1 

4 

7 

Figure 1. Drawing showing side and top view of seabeddrifter-------------------------------

2. ~ap showing seabed drifter release locations, 5-6 ~arch 1970--------------------

3. ~ap showing locations of releases and approximate recovery positions of 

seabed drifters released in the Pacific Ocean-----------·-----------------------

4. ~ap showing locations of releases and approximate recovery positions of 

seabed drifters released within the bay system---------------------------------

TABLES 

Table 1. Recovery statistics of seabed drifter releases------------------------------------

2. Directional data of seabed drifters ----------------------------------------------

III 

Page 

82 

3 

5 

6 

Page 

84 

4 

A PRELIMINARY STUDY OF THE EFFECTS OF WATER CIRCULATION 

IN THE SAN FRANCISCO BAY ESTUARY 

Movement of Seabed Drifters in the San Francisco 

Bay Estuary and the Adiacent Pacific Ocean: 

A Preliminary Report 

By T. J. Conomos, D. H. Peterson, P. R. Carlson, and 

D. 5. McCulloch 

INTRODUCTION 

Man's increasing utilization of the San Francisco 

Bay estuary and the adjacent Pacific coast has made, 

and will continue to make, it necessary to increase 

our knowledge of the processes and rates of sediment 

transport within the San Francisco Bay system and 

in the nearby coastal Pacific. 1 (Note: numbered items 

in text are keyed to numbered items in appendix at 

end of chapter B.) The m o v em en t of near- bottom 

water is of considerable importance in transporting 

suspended materials between the Pacific Ocean and 

the San Francisco Bay system. Owing primarily to 

tidal flow, the movement of near-bottom water may 

be oscillatory. There is, however, a residual drift. 2 

To describe this residual drift, the U.S. Geological 

Survey is releasing seabed drifters bimonthly within 

the San Franscisco Bay system and on the continental 

shelf of central California from Cape Mendocino to 

Point Conception. 

This report presents preliminary r e s u 1 t s of the 

first release (5-6 March, 1970) but considers only 

those seabed drifters released in the Bay system 

and on the continental shelf within 90 kilometers 

of the Golden Gate. All releases were made in water 

depths of less than 180 meters (100 fathoms). Only 

the direction of residual drift is considered. When 

recovery data are more complete for this and future 

releases, the rates of flow will be determined. 

METHODS 

The seabed drifter used in this study 3 closely conforms to that used by in v e s t i gator s on both the 

B1 

Atlantic and Pacific coasts.l,'+,s,s,7,a It consists of a 

perforated plastic saucerlike disk on a 55-centimeterIon~ plastic stem, with a 5-gram brass collar attached at its lower end (fig. 1). With the collar the 

average density of the drifter is greater than that 

of water. In nonmoving water the stem tip rests 

lightly on the bottom with the saucer off bottom; in 

currents the saucer leads the stem in moving downstream, and the drifter tends to lift off the bottom.6 

The drifters were released within the Bay system 

from a boat; offshore drifters were released from 

an aircraft flying at an altitude of 150 m, and at a 

speed of 150 km per hr. Release locations are 

shown in figure 2. To assure rapid sinking and minimal transport from other than bottom currents, the 

drifters are held in clusters of five and weighted by 

a ring of salt around their stems. The salt weights 

dissolve within 45 minutes. Groups of drifters in 

multiples of 25 were released at each station (fig. 2). 

The releases were completed during the daylight 

hours on 5 and 6 March, 1970; offshore releases 

within 30 km of the Golden Gate were made during 

an ebbing tide. Aircraft release points were located 

by time and course from the coast and boat releases 

by navigational (visual and radar) fixes. 

RESULTS 

Of the 1,345 drifters released, 18 percent (237) 

were recovered by 22 April 1970 (table 1). Eighteen 

percent of those released within the Bay system (including the Golden Gate reI ease points) were recovered; 17 percent of those released offshore were 

recovered. The release and recovery information 
SERIAL----

NUMBER 

0 

0 0 

0 

DISC~ (YELLOW) 

---sTEM 

(RED) 

55 em 

SEABED DRIFTER 

(WOODHEAD TYPE) 

Figure 1.-Side and ·top view of seabed drifter. Modified from a 

drawing by J. B. Zocchi. 

B2 
38"30 1 

37"30 fRELEASE LOCATIONS 

.t:._35 RELEASE DATES NUMBER RELEASED 

5 March 6 March 

0 25 

0 50 

75 

:~ NUMBERS INDICATE PERCENTAGE OF RECOVERIES 

oo AS OF 22 APRIL 1970 

10 20 30 40 

Kilometers 

0 10 15 20 25 30 

Miles 

ISOBATH VALUr::S EXPRESSED IN FATHOMS 

123'00 

...L 

122"30 

...L 

122'00' 

Figure 2.--Seabed drifter release locations, 5-6 March~l970. The 

number adjacent to each symbol indicates the percentage of 

drifters recovered (as of 22 April,l970) that were released 

at that location. 

BS 

50 

-, 

-1 

-1 

35 

121°30' 
Table l.--Recovery statistics of seabed drifter releases 

Total number of seabed drifters 

Location Released Recovered 

(5 and 6 March, 1970) (as of 22 April, 1970) 

Recoveries 

(percent) 

Outside bay-------------

Inside baya ____________ _ 

Total-----------------

575 

770 

bl,31+5 

97 17 

11+0 18 

237 18 

a Includes Golden Gate release positions. 

b One release group contained 20 drifters, not the usual multiple of 25. 

Table 2.--Directional data of seabed drifters 

Drifters released 

Drifters recovered Outside bay Inside bay 

Number Percent Number Percent 

Inside Bay---------------- 57 59 136 97 

Outside Bay--------------- 1+0 1+1 3 

Total------------------- 97 11+0 

a All four were released at the Golden Gate. 

for the bottom drifters given in table 2 shows that, of 

those recovered, 19 percent ( 44) were found on the 

ocean beaches seaward of theGoldenCate, and81 percent ( 193) were found inside the Golden Gate. The percentage recovery tabulated for each release point is 

shown in figure 2. 

The principal directions of drifter movement are 

shown in figures 3 and 4. The arrows are drawn from 

release points to recovery locations typical of that 

release point. Not all recovery points are shown. 

Drifters released in the Pacific moved predominately 

toward the east. Movement of drifters into the San 

Francisco Bay system (San Pablo Bay) is particularly 

apparent for offshore releases less than 25 km from 

the Golden Gate, at which the bottom depth is generally 

less than 30m (17 fathoms). Excluding the data from 

release points at the Golden Gate (inset in fig. 2), no 

drifters released within the Bay system have yet been 

recovered on the ocean beaches (fig. 4, table 2). 

The Bay system can be divided into three areas on 

the basis of differing seabed drifter movements (fig. 4). 

1. Rio Vista westward to eastern San Pablo Bay: 

Dominant movement was southwesterly. Typical maximum transport distances are 75 km. 

B4 

2. Southern San Pablo Bay, northern San Francisco 

Bay: Dominant movement was to the north 

and west, with maximum transport distances 

of 40 km. Recovery was greatest from releases in San Pablo Bay. 

3. South San Francisco Bay: Little apparent net 

movement ( < 8 km) and no prevalent direction. The percentage of recovery was lowest 

in this area. 

DISCUSSION 

Although the data presented herein represent preliminary results of the initial release, results of 

similar seabed drifter studies and a basic knowledge 

of physical processes occurring in this system allow 

us to tentatively explain several phenomena. 

The decrease of drifter recoveries with increasing 

depth on the continental shelf suggests a net seaward 

drift that becomes more important farther offshore. 

Similar drifts have been reported along the middle 

Atlantic and northwestern continental she 1 v e s.4 ,

7 

Drifters that traveled east were respondingprimarily 

to the effect of onshore wave transport. With more 

recovery data we should also be able to define the 

direction of longshore drift. 
l8"30 1 

f38"00 f-

·. 

f- 10 

Farallon Is 

.. 

20 30 

K1lometers 

10 

__l_ 

123"00 

15 20 

Miles 

25 

_L 

40 50 

30 35 

_L 

122')0 

T 

SAN JOSE 

PACIFIC OCEAN RELEASES 

5 MARCH-22 APRIL 1970 RECOVERIES 

_L _L 

122'00 

Figure 3.--Locations of releases and approximate recovery positions of seabed drifters released in the Pacific Ocean. 

B5 

I 

121"30 
38"30 1 

37"30 f0 

10 

10 

_j_ 

123"00 

20 30 

Kilometers 

15 20 

Miles 

40 50 

25 30 

_L 

35 

_L 

li!Z•JO' 

SAN JOSE 

BAY SYSTEM RELEASES 

5 MARCH-22 APRIL 1970 RECOVERIES 

Figure 4.--Locations of releases and approximate recovery positions of seabed drifters released within the Bay system. 

B6 
The dominant transport of drift e r s into the bay 

through the Golden Gate is consistent with the circulation pattern typical of estuaries. 9 When fresh water, 

provided mainly by the Sacramento River runoff, is 

mixed with sea water, it forms a low-salinity, lowdensity upper layer, which tends to move seaward. 

Sea water at depth tends to move toward the river 

to replace the salt and sea water that have been entrained or mixed upward into the surface outflow. 

This basic circulation pattern occurs in the northern 

portions of the Bay system and in the adjacent ocean. 

The landward transport of drifters in these areas 

apparently reflects the movement of the high-salinity 

bottom water. A similar estuarine circulation pattern 

has been documented by seabed-drifter data in Narragansett Bay, Long Island Sound, Raritan Bay, 

Delaware Bay, 4 the Columbia River estuary, s and the 

Straits of Juan de Fuca and Georgia. 7 

The strong northward flow from south San Francisco 

Bay which is evident southeast of the Golden Gate ( releases at the San Francisco-Oakland Bay Bridge) is 

more difficult to explain in terms of circulation observed in other major estuaries. However, the southern part of San Fran cisco Bay is atypical in that it 

has only a very small supply of fresh water at its head. 

The observed northward drift is apparently due to the 

flushing action in the southern part of San Francisco 

Bay related to the high discharge of the Sacramento 

River during this period.1 0

, 1 1 During flushing a lobe of 

low-salinity, low-density surface water moves southward and displaces a portion of the more saline water 

which is present in the southern bay. The displaced 

water moves in a northerly direction where some of 

it is entrained in the sea water which is moving towards the river. A small net movement and a lack of 

a prevailing drift direction in the southernmost parts 

of San Francisco Bay indicate sluggish movement of 

the bottom water. The sluggish movement also is indicated by data summarized by Lager and Tchobanoglous.1 2 

The transport of drifters from Rio Vista to the San 

Pablo Bay is a manifestation of the direct influence of 

the river inflow at the head of the estuarine system. 

The convergence of drifters on the south shore of San 

Pablo Bay apparently marks the broad area where 

the predominately seaward-flowing (river inflow) and 

predominately landward-flowing (salt-water inflow) 

bottom waters converge and reach dynamic equilibrium during early spring. This area may correspond 

to the nodal points of sediment accumulation which 

have been described in At 1 antic coastal plain 

estuaries.1 3

• 1 4 

APPENDIX 

1. Since 1968, the Office of Marine Geology and the 

Water Resources Div. of the U.S. Geol. SurB7 

vey have conducted an investigation of the geology of San Francisco B~y. Study has been directed toward (a) the bedrock basin and overlying sediments and (b) themoderndepositional 

environment. The principal aim of the latter 

is to understand the relation between the chemistry and circulation of the bay water, and the 

origin, transportation, and disposition of the 

suspended and bottom sediments. Monthly sampling at reoccupied stations since January 1969 

has included: 

( 1) Salinity, conductivity, temperature, and 

turbidity (percent light transmission). All 

measured throughout the water column. 

(2) Water samples (2-meter depth) examined 

for suspended particles, silicate, phosphate, nitrate, nitrite, and dissolved and 

particulate carbon. 

2. Residual drift is defined herein as the net motion 

experienced by a body of water during a given 

period. 

3. Woodhead, P. M. J., and Lee, A. J., 1960, A new 

instrument for measuring residual currents 

near the sea-bed: Conseil Internat. Explor. 

Mer, Hydrog. Comm., Ann. Mtg., Moscow, 

1960, 6 p. 

4. Bumpus, D. F., 1965, Residual drift along the 

bottom on the continental shelf in the middle 

Atlantic Bight area: Limnology and Oceanog., 

v. 10 (Supp.), p. R50-R53. 

5. Lee, A. J., Bumpus, D. F., and Lauzier, L. M., 

1965, The sea-bed drifter: Internat. Comm. 

Northwest Atlantic Fisheries Research Bull., 

v. 2, p. 42-47. 

6. Morse, B. A., Gross, M. G., and Barnes, C. A., 

1968, Movement of seabed drifters near the 

Columbia River: Am. Soc. Civil Engineers 

Proc., Jour. Waterways and Harbors Div., 

v. 94, no. WW1, p. 93-103. 

7. Gross, M. G., Morse, B. A., and Barnes, C. A., 

1969, Movement of near-bottom waters on the 

continental shelf off the northwestern United 

States: Jour. Geophys. Research, v. 74, no. 28, 

p. 7044-7047. 

8. Squire, J. L., Jr., 1969, Observations on cumulative bottom drift in Monterey Bay using seabed drifters: Limnology and Oceanog., v. 14, 

no. 1, p. 163-167. 

9. Pritchard, D. W., 1955, Estuarine circulation 

patterns: Am. Soc. Civil Engineers Pro c., 

v. 81, no. 717, p. 1-11. 
10. Peterson, D. H., and Carlson, P. R., 1968, Influence of runoff on seasonal changes in salinity of San Francisco Bay: Am. Geophys. 

Union Trans., v. 49, p. 704. 

11. Chapter A of this circular. 

12. Lager, J. A., and Tchobanoglous, George, 1967, 

Use of hydraulic and mathematical models for 

determining effluent d iff u s ion in South San 

Francisco Bay: Natl. Symposium on Estuarine 

Pollution, Stanford Univ., Stanford, Calif., 1967, 

Proc., p. 384-422. 

B8 

13. Meade, R. H., 1968, Relations between suspended 

matter and salinity in estuaries of the Atlantic 

Seaboard in Geochemistry, precipitation, evaporation, soil, moisture, hydrometry-General 

Assembly of Bern, 1967, Reports and discussions, v. 4 : Internat. Assoc. Sci. Hydrology 

Pub. 78, p. 96-109. 

14. Meade, R. H., 1969, Landward transport of bottom sediments in e stu a r i e s of the Atlantic 

Coastal Plain: Jour. Sed. Petrology, v. 39, 

no. 1, p. 222-234. 

U. S. GOVERNMENT PRINTING OFFICE : 1970 0 - 389-708