Investigating the human impact on the Bay environment

Presenter: Kent LIghtfoot

Today it is my pleasure to discuss the issue of human-environment relations in the San Francisco Bay from a long-term perspective.  The study of the diachronic relationship between humans and their environments is known as historical ecology.  It is important to examine the historical ecology of the San Francisco Bay Area, as it may alter some of our ideas about the San Francisco Bay.

If asked when humans began to impact the local area, most people would respond that human impact is fairly recent, perhaps in the late 19th and 20th centuries.  During that time, we see evidence of:

  • agricultural activities
  • diking of the bay shore
  • hydraulic mining debris from the Sierra Nevada Mtns
  • land reclamation and urbanism
  • disposal of pesticides, domestic and industrial wastes

Prior to 1850, before Anglo-American colonization, it is not uncommon for people to imagine the San Francisco Bay as a pristine wilderness.

The primary purpose of my talk is to have you rethink this, and begin to consider the Bay as a very old anthropogenic landscape.  The ecology of the Bay has been shaped by humans for many centuries.  We cannot consider the ecology of the bay since its very formation without taking account of humans.  I argue that there never has been a truly natural or pristine San Francisco Bay.

Today I will make four basic points about the Historical Ecology of the Bay, from early prehistoric times through the early colonial period when Spanish, Mexican, and Russian peoples colonized the area.

I.  Local native peoples were here during the creation of the San Francisco Bay system.

As discussed earlier this morning, the greater SF Bay was created only in the last 11,000 to 10,000 years as a consequence of the post-Pleistocene sea level rise.

  • Archaeological research in the region shows evidence of human occupation, for example:
  • Up on the Sonoma County coast – Duncans Landing site
  • Los Vaqueros area in Alameda County
  • Sites in Santa Clara County

These sites provide ample evidence that local hunter-gatherer peoples, native Californians, occupied the area when the Golden Gate was first inundated by rising sea waters about 10,000 years ago.

This is rather significant when you think about it.  Native peoples witnessed the creation and expansion of the San Francisco Bay system!  I think about the stories told over countless nights around campfires, in oral traditions handed down from one generation to another, that may have described the growth of the great bay.

So people were here from the very first.

II.  Once the rate of sea level began to decline and the current bay shore began to emerge, human habitations began to dot the landscape.

Most estimates of sea level rise suggest rapid expansion of the Bay system from 10,000 to 6,000 years ago.  About 6000 years ago, sea level rise began declining, and expansion of the bay took place at slower rate.  At this time, the current configuration of San Francisco Bay, San Pablo Bay, and Suisun Bay began to emerge. Thousands of acres of intertidal mud flats and salt and brackish tidal marshes were beginning to take root and thrive during the period of 6000 to 2000 before the present.  The chronology of archaeological sites tends to follow the establishment of tidal wetlands around the Bay.  The earliest Bayshore sites date to about 5000 to 4000 years ago.

The kinds of archaeological sites that were created are rather unique.  They’re known as shell mound sites.  Many of our observations of these impressive sites are from early UC Berkeley archaeologists (Max Uhle, Nels Nelson and others) beginning with excavations in 1902.

Below are mages of a shell mound in Emeryville, CA, excavated by Max Uhle. Click to zoom in on each image.

Emeryville mound, 1907.

Open cut on the western side of the mound, 1907.

Southerly wall of areas 34 and 40, looking north; 1924 demolition of the mound.

Cross-section of the western foot of the shell mound.
Images © Phoebe A. Hearst Museum of Anthropology

There are several characteristics of shell mound sites.


  • The mounds are built up from tons and tons of rock, soil, ash, and shell.
  • They vary greatly in size: the largest ones cover two football fields laid end-to-end, and are 30 feet high.


  • Human remains have been exposed in all cases where large mounds have been excavated.
  • The remains are often deep in the core of the mound.
  • Many mounds contained several thousands of graves, a key observation.


  • In large mounds that have been extensively excavated, we find house floors, hearths, roasting pits and other “domestic” features.
  • The houses have circular floor plans, are often saucer shaped – 3 to 5.5 meters in diameter, and are of hard packed clay – 7 - 10 cm thick


  • The mounds contained a diverse range of lithic, shell and bone artifacts.

Archaeologists have proposed various interpretations for shell mounds.  Early UC Berkeley archaeologists proposed the interpretation of  “kitchen middens” or “rubbish dumps”.  Later archaeologists have added two other possible interpretations:  Specialized cemeteries, where mortuary ceremonies and feasting rituals took place, or mounded villages, with ancestors buried below, and people living on top of mounds.

No matter how you interpret mounds, it is clear that these were not just ephemeral campsites.  They were very sizeable mounded structures.

III.  It is clear that prehistoric native peoples had some kind of impact on environment of the greater SF Bay.

The large size and number of shell mounds suggest a fairly large population of Native Californians.  Initial survey work by Nels Nelson recorded 425 large mounds dispersed around the bayHe did not locate all of them, because unfortunately urban expansion destroyed many of them.  Furthermore, a regional settlement pattern characterized by mound clusters shows that where freshwater empties into the Bay, we find not just one or two mounds but often a cluster of between 4 to 6 mounds.

It is difficult to estimate population density very precisely at this time.  On one hand, not all of these mounds were probably occupied at the same time.  But on the other hand, many appear to have been used over multiple centuries.  There were overlapping occupation spans.  Certainly when early Spanish explorers entered the Bay Area between 1769-1775, they described very dense population, with smoke rising from many villages around the Bay.

What is clear is that a diverse range of resources were being exploited by Bay Shore peoples.  This is borne out by archaeological studies of faunal or animal remains in the shell mounds.  These remains include:

  • Lots of shellfish:  Bay Mussels (Mytilus trossulus /edulis), Pacific Oyster (Ostrea lurida), Bent-nose clam (Macoma nasuta).
  • Terrestrial mammals, including elk, black-tailed deer, and pronghorn; these would have been hunted with darts or bow and arrow. We also see wolf, fox, bear, skunk, and raccoon.
  • A diverse range of fish remains, including bat rays, green and white sturgeons, king and silver salmon, sharks, surf perches, jack smelt.  Fishing was a major activity.  They probably used a hook and line, nets (dip nets, seine nets with weights), and tule balsas (on display at Coyote Hills Regional Park).  Tule balsas were built of tule bundles wrapped together; they would hold 1, 2, or 3 people and use double bladed paddles—they were not for ocean voyages.
  • Sea mammals, such as sea otters, harbor seals, fur seals, and sea lions.  They would have been hunted with spears, darts, nets, clubs.
  • Birds, in very high numbers, especially water fowl such as ducks, geese, cormorants, loons, and grebes.  They were probably captured with nets, using tule decoys.

In considering the overall impact that Native Californians had on SF Bay ecology, there are two schools of thought.


This perspective questions the old idea of California Indians as passive hunter-gatherers who simply collected the fruits of a “wild” and “pristine” land.  Kat Anderson, Thomas Blackburn, Lowell Bean and others view California Indians as nurturing land managers who constructed a “cultivated” landscape through deliberate human intervention over many centuries.

They proposed that native peoples created and maintained various kinds of productive habitats through techniques including fire management (burning), tillage, pruning, broadcasting of seeds, weeding, and conservation practices.   Highly skilled in enhancing wild resource production, they created grasslands and open oak parklands through manipulation of the environment.


Proponents of this theory present a darker, more complicated story of prehistoric hunter-gatherers.  It was first suggested by early Berkeley archaeologists, who noted that shell mounds contained large numbers of mollusk remains, which must have had an impact on local shellfish beds.

Their point comes into sharper focus when you consider that one mound, such as Ellis Landing, is estimated to contain more than 17 million mollusk shells (Nelson 1909:346).  That’s quite a few clam bakes!

Early Berkeley archaeologists noted a pattern in shellfish frequencies in excavations:  bay mussels and oysters tend to be found at lowest levels, while clams are found in younger or upper levels.  But there is considerable variation, reflecting local changes in estuarine habitats.  They argued that the change from mussel and oyster to clam may have been caused by various factors, including changes in the tastes of Indians and changes in the environment (silting of the bay would be ideal for burrowing clams).  But it could also suggest the idea that overexploitation of shellfish beds forced them to shift to different kinds of mollusks as favorite food sources disappear from some bay habitats.

The major advocates for this position, Jack Broughton and Dwight Simons, have examined faunal remains from various shell mounds.  Their research results show a shift over time (in Late Holocene), from large prime animals to smaller game.   Lower (earliest) strata contain large numbers of big “fat” artiodactyls (deer, elk, pronghorn) and large fish (such as white and green sturgeon), while these decrease in frequency in upper (later) strata.  They are replaced by increasing numbers of smaller game, such as sea otters and small species of fish.

Their interpretation is that when large terrestrial game and sturgeons (optimal prey because they are big food packages) were hunted or fished out, people were forced to turn to smaller, less optimal food packages including sea otters and small fish.  At these times they also observe more emphasis on acorns and birds.

While many factors may account for these changes in faunal remains, most archaeologists who advocate resource intensification argue that the primary reason was population growth, which created resource stress and forced people to go after secondary resources.

I feel that these two perspectives (Resource Managers and Resource Intensification) are NOT mutually exclusive.  There were probably elements of both taking place through space and time.   The critical point is that these perspectives do not view the prehistoric San Francisco Bay area as pristine wilderness.  It has long been very much a human altered landscape and seascape.   Both viewpoints support the idea of natives creating an anthropogenic landscape.

IV. The environment of the Bay Area underwent significant shift in its anthropogenic landscape with the early colonization by Spanish and Russian settlers.

The Spanish colonization of the Bay Area began in 1776, when Spanish soldiers and Franciscans began to build presidio and missions.  They implemented a program of missionization among native peoples, and developed extensive agricultural ranches and farms.

What one sees with the coming of the Spanish and later Mexican settlers is the transformation of one anthropogenic environment to another. The Native Peoples (Ohlones, Coast and Bay Miwok) were aggregated into the missions.  The Spanish no longer allowed them to burn grasslands, so they were no longer maintaining native grasslands and open oak woodlands.  The Indian manipulated landscape was replaced by an agrarian one.

The late 1700s and early 1800s unleashed a plethora of Old World animals and plants into the environment.  Thousands of cattle, sheep, and horses grazed around the Bay, and thousands of acres of wheat and barley fields, orchards and vegetable gardens were cultivated.

The most devastating aspects of the new introductions were that various pests, such as pigs and rats, were unleashed into the environment.  Alien weeds thrived in the new environment, especially with intensive grazing.  Archaeological research on pollen and macrobotanical remains from archaeological contexts, especially in the adobe bricks of missions, shows rapid colonization of weeds (various types of thistles, curly dock, cheeseweed, and wild oat).  These began to out-compete indigenous grasses.

It is not clear how this initial Spanish colonization effected Bay Area waters, though there is some evidence of increased sedimentation in coastal estuaries during Spanish times, which appears to be related to over-grazing and run-off.

It is interesting to note that Russian colonization did have an impact on the Bay.   Russians colonized Fort Ross from 1812-1841 in a trade outpost.  It generated significant economic activity from sea mammal hunting, specifically sea otter.  They used Native Alaskans (baidarkas, “wolf packs”).  They began hunting along the Sonoma and Marin coasts, portaging along Point Bonito on the Marin Headlands to the SF Bay.   The SF Bay contained thousands of sea otters, which represented a rich hunting area for the Russians.   They began their hunting illegally, sneaking into Spanish waters. 

The Russians increased their harvest when Mexico took over administration of California in 1821.  They negotiated a contract allowing the Russians to hunt sea otters.  They exterminated the population, along with other sea mammals such as harbor seals and sea lions.  This had a potentially major impact on the Bay, as sea otters are a “keystone” predator with voracious appetites. They consume 25% of their body weight each day, and their preferred foods are sea urchins, crabs, clams, and abalones.

Studies of sea otters in Alaska show that when otters disappear, it affects marine productivity.   Sea urchins and other herbivorous invertebrate populations increase, and they in turn consume kelp forests that support fisheries.  Thus the decrease in sea otter population results in the degradation of kelp forests and local fisheries.

It is not clear what happened in the SF Bay, but when the SF Bay sea otter population was wiped out by the 1830s and 1840s, it must have had a real impact on clam and crab populations, causing a major growth spurt.  It is even possible that prehistoric hunting of sea otters may have decreased population enough to allow the clam population to grow unchecked, which could explain why we see a preponderance of clam in late prehistoric shell mounds.

The point to keep in mind is that human impact on one component of the ecology of the Bay can have significant effects on others, which we need to think about.

V.  The critical point of my talk is that the San Francisco Bay is an excellent setting in which to view the symbiotic relationship of humans and the environment over the last 11,000 years or so.

If we think about it in terms of the creation of anthropogenic landscapes, the San Francisco Bay has been undergoing transformations for many centuries.  What we see today in the SF Bay is part of a long-term process, in which human modification to the local environment is accelerating at an unprecedented pace.