Natural History of Mission Bay

Historical Essay

by Chris Carlsson

Mission-Bay-c1700-by-Mark-Brest-van-Kempen 7786ps.jpg

View of Mission Bay (Potrero Hill at right of Mission Creek) from Corona Heights above Castro and 15th as it probably looked around the year 1701... Photo below taken 2001 from approximately same location.


Image by Mark Brest van Kempen, bottom photo, 2001: Mark Brest van Kempen Funded in part by a grant from The Creative Work Fund.

All that’s left today of the original Mission Bay is the Mission Creek channel, extending from San Francisco Bay past the Giants Stadium to under the freeways near 7th and Berry Streets. Mission Bay was an estuary, combining freshwater marsh, saltwater marsh, tidal mudflats, and shallow bay. Nearest its original shoreline in what we now think of as the relatively flat South of Market area were acres of swampy bogland between large sand ridges that had blown in from the ocean over thousands of years. It was a relatively tree-less landscape. In what is today the north Mission part of town, freshwater streams poured down from the eastern flanks of Twin Peaks to mix with tidal surges through the Mission Creek wetlands that filled the area from approximately today’s 19th Street on the south, Guerrero and Valencia on the west, and Division (where the elevated freeway is now) on the north. While there were some willows along the banks of the main channel of Mission Creek, there were few trees in this area either. San Francisco’s original landscape was largely scrub-covered dunes in the valleys on either side of the large northwestern diagonal of Franciscan bedrock that underlies our tallest hills (running from Hunters Point in the southeast through Bernal Heights, Mt. Davidson, Twin Peaks, and Mt. Sutro, and out to Lands End and the Golden Gate in the northwest corner of the City).

Mission Bay was bracketed by Rincon Hill and South Beach on the north, and Potrero Point to the south. Fresh water bubbled from artesian springs on the northern slopes of Potrero Hill to tumble into Mission Bay. A great quantity of fresh water poured in too from Mission Creek, whose mouth was approximately between today’s 7th and 8th Streets around Berry Street. That fresh water emerged from two tributaries, one that started on the slopes of Twin Peaks near today’s Corbett and Clayton Streets, and the other that began not far west of today’s Market and Church Streets, running down 14th, under the Armory and into the tidal wetlands that made up a great deal of the north Mission in pre-urban times. An underground river of fresh water that still moves southeasterly through the subterranean soils of the City’s Civic Center area surfaced in countless ponds and swampy bogs from Mission Street all the way to the edges of Mission Bay proper. This added millions more gallons of fresh water every week to the saltwater Mission Bay. This area teemed with a wide variety of life.

We tend to think of such a “natural history” as something that evolved separate from human intervention, but all the new anthropology and archaeology of the Americas prior to 1492 indicates a remarkably anthropogenic landscape.(125) That is to say, the people who lived here for thousands of years before the last two centuries were not just idly consuming the natural riches of the area, but were undoubtedly fully engaged in shaping that environment to suit their needs and preferences, using everything from seasonal burnings to careful cultivation of plants and environments that were conducive to abundance of food and resources. A food-rich, accessible estuary like the one that occupied this eastern shore of the San Francisco peninsula was managed too, but in ways that are difficult to reconstruct.

In fact, the wet, shifting geography of the tidal zones makes a full archaeological investigation quite difficult, and the extensive landfilling along historic shorelines destroyed the earth mounds and shellmounds that once existed in this zone. We know that pre-contact dwellers here lived in small seasonal villages. Shellmounds and other middens could be found around San Francisco bay along nearly every creek and river—sites holding generations of discarded shells and other “household” debris, which were usually also burial sites. Typically the shellmounds and related earth mounds would be near the mouths of creeks where they opened into the bay, and sometimes a bit further up the waterway towards higher land. Unfortunately, any evidence of shellmounds around Mission Bay was destroyed during the early, pell-mell urbanization process, long before they became interesting to anthropologists. Within a couple of years of the Gold Rush, the shoreline of Mission Bay was already being radically altered by shipbuilding and other early industries, and “making land” by dumping sand, rock and debris from the hills that were being leveled in the nearby South of Market area. The adjacent lands were being built upon and urbanized as fast as landowners could manage it. A natural landscape was scraped away, covered over, and ripped apart to make space for the new city of San Francisco.

The physical landscape of Mission Bay prior to this radically invasive and destructive form of habitation was like most of the San Francisco Bay. Writing in 1909, N.C. Nelson described the deep silting of the bay around its entire fringe: “Almost the entire bay is fringed with a belt of tide-land, salicornia marsh, which attains a width of from three to five miles at the extremities and is absent only in the constricted central portion.”(126) This marsh typified the areas adjacent to the open waters of Mission Bay too. Freshwater marshes prevailed further from the open water, and as the freshwater poured into the saltier areas it would rest on the surface, since it is lighter, before mixing into a brackish stew.

A Botanical Reminiscence

It’s difficult enough to imagine San Francisco’s Mission Bay as an open expanse of bay water, ebbing and flowing over rich mud flats with the daily tides. Our imagination is challenged even further when we include the flora and fauna that flourished in this area prior to the arrival of European settlers. We don’t know exactly what was here, but luckily we have the observations of Hans Herman Behr, a young physician and naturalist who settled in San Francisco originally in 1850, and wrote down his observations some forty years later.(127) He describes freshwater ponds that pocketed the zone around today’s 7th and 8th Streets near Harrison:

Near the formerly well-known Russ Gardens there were extensive marshes abounding especially about their borders in interesting plants.(128) Here grew the large-flowered dogwood, buckbean, stream orchids, the delightfully fragrant white-flowered bog orchid, and cotton grass. In the same vicinity I found in a single locality five specimens of leather grape-fern and the lady fern grew luxuriantly, often forming rootstocks two feet high, simulating tree ferns.

In this lengthy excerpt he describes what he found in a study area bounded by today’s Market and Mission, 6th and 7th Streets:

The landscape which extended in the years 1850 to 1860 from Mission Creek to (Rincon Hill) was in its greater part filled by swamp and bog and Salicornia flat. A turfy fresh-water formation, inland, gradually merged into the Salicornia flat and was crossed by the serpentine courses of the tide creeks. This formation was the basis for a system of sand downs overgrown by shrubbery, or occasionally arborescent vegetation. The downs were mostly arranged in parallel ridges, the ridges being most numerous and frequently confluent towards the mouth of Mission Creek. In a locality which is now bordered by Sixth and Third Streets [there was] a very deep, boggy branch, the sand down region, [south of] what is now Mission Street. The ridges which enclosed this branch were higher than the rest and reached in considerable elevation the line of Howard Street, where they formed a very abrupt boundary between sand and bog.
The deep, boggy branch that crossed Mission Street, where the swamp formed a valley encircled by deep downs, was the seat of a peculiar, now almost extinct Flora, at least as regards the neighborhood of San Francisco. This locality was the only one inhabited by the now extinct Arenaria palustris, which grew there in company with Spotted Water Hemlock,(129) Evening Primrose, Water Pennywort, Pond Lily, and Cattails. An arm of this swamp, then inaccessible even to cows, followed the side of Howard Street, down, bordering the flat as far as what is now Fifth Street, where it became overgrown by arborescent vegetation and ended in a thicket of California Wax Myrtle, Blueblossom Ceanothus, Coast Silktassel, and several kinds of fern including Chain Fern and Aspidium munitum, the latter with almost arborescent trunk.
Where subterranean water courses approached the surface, luxuriant branches of Douglas Baccharis, Philadelphia Fleabane, local Asters, and Rosilla covered the ground, occasionally overspread by the flowering Twin-berry with its shining black berries in their dark red involucres, or Elderberry and wild currants.
The bog itself was perceptibly lower at the foot of the hills than towards its center, which was occupied by a characteristic swelling of the turf. [That] gave origin to a net of interwoven little water-courses, permeating a kind of meadow and themselves covered by a moss-like carpet of an aquatic fern… It was a kind of Arctic oasis amidst a vegetation of California type. Where the water collected into small rivulets, it became hidden under the dense, mossy, and very deceiving carpet of aquatic fern. The turf consisted to a great extent of sedges.(130) Out of this turf emerged the fragrant Bog Orchid and Buckbean and, in one locality, Stream Orchid, with Californian Blue-Eyed Grass. These were the most conspicuous and at the same time the most frequent plants of the formation. Where the rivulets approached and extended to the serpentine course of the tide water creek, the formation changed; the aquatic fern carpet dissolved into floating islands before disappearing entirely, the grasses and sedges lost their dense turfy appearance and developed higher stems with more conspicuous inflorescence and fewer leaves. Only on the margin of the creeks was developed the characteristic luxuriant turf of salt grass, frequently grown over by gumplant.
Then followed the Salicornia flat, here and there ornamented by Salt Marsh Bird’s Beak and Seaheath, abruptly ending in a boggy marsh without any vegetation. Here was the mouth of the serpentine creek, the receptacle of all the watercourses of the flat. The mouth of the creek was bordered on its left side by a flat ridge of coarse, dry sand without grass, but sparsely overgrown by Seaheath, California sea-lavender and Monkey Tail.
Common plants of the saltwater marsh that were prevalent in this area include Cordgrass, a great contributor to the estuary ecosystem through its steady decomposition into the mudflats, providing a rich source of food for worms and snails that are in turn the major food for fish and birds. Inland from the Cordgrass area is a belt of succulent plants, in particular Pickleweed, which absorbs water and salt. Along with Saltgrass and similar plants, salt is secreted back into the surroundings from their leaves or by dropping pieces into the water below. Detritus and mud are trapped in the root systems which are rich nutrient sources for the life of the saltmarsh.

Animals around Mission Bay

One of the best anecdotal accounts describing wildlife along the shore takes place just north of Mission Bay in the then-unfilled Yerba Buena Cove. William Richardson was the first person to build a home near the shore in today’s San Francisco back in 1837. It also served as the center of his thriving business as a middleman between the cattle economy of the Missions (mostly produced with enslaved Indian labor) and the visiting sailing ships from Britain, Russia, France, Spain, and eventually Mexico and the United States. His son Stephen wrote in his own memoir, Days of the Dons:

One thing about the cove of Yerba Buena, or San Francisco, as it very soon came to be called, was the great number of good-sized fish that swam close in shore and were stranded by the outgoing tide. These were the natural food of all sorts of predacious animals, which existed in enormous numbers and, being little interfered with by man, for that reason were indifferent to his presence. I often used to sit on the veranda of my father’s house and watch bears, wolves and coyotes quarreling over their prey along what is now Montgomery Street.(131)

Animal bones found in the shellmounds excavated in the early 20th century give us a view of what lived here, and what was eaten here too—deer, elk, sea-otter, beaver, squirrel, rabbit, gopher, raccoon, badger, skunk, lynx, bear, seal, sea-lion, porpoise, turtle, wolf, goose, cormorant, canvasback ducks.(132) The most commonly discovered molluscan remains in the shellmounds were the “soft-shelled” clam and the “soft-shelled” mussel.(133)

Threespine Stickleback and Steelhead Trout spawned in Mission Creek. Massive runs of sturgeon and salmon filled bay waters, occasionally becoming beached on the mudflats as the tides went out. When the tide is in, the mudflats beneath the water come to life. A specialized worm called the Innkeeper lives in a u-shaped burrow with two entrances up to three feet apart. A funnel-shaped slime net inside traps detritus and plankton, its main foods. One of its cohabitants (hence the name Innkeeper) is the Arrow Goby, a two-inch fish that hides out in its burrow, sometimes five or more at a time. The California Ghost Shrimp is another ubiquitous resident of the mudflats, helping the rest of the mudflat dwellers by their busy digging and oxygenating of the mud.(134) A variety of snails and slugs live on the surface of the mud too. The most common snails are the California Horn Shell, the Cloudy Bubble Snail, and the Channeled Dog Whelk. The Bay Sea Hare, or Sea Slug, can be as much as six inches long, is a bright yellow with blue dots on a brown background, and feeds on other snails from its preferred zone at the far end of the mudflats furthest towards the open water.


A portrayal of what Mission Bay probably looked like from the shores of Potrero Hill, c.1701.

Image by Mark Brest van Kempen. Funded in part by a grant from The Creative Work Fund.

Bird life on Mission Bay was inconceivably thick. Mission Bay was a happy hunting ground for ducks, geese, herons, egrets, Clapper Rails, Marsh Wrens, American Bitterns, Northern Harriers, and many migratory birds. The snails, slugs, and other mud-dwelling critters were the ideal food for many of the birds who filled the skies and the waters. In the mudflats, birds with differently shaped bills of different lengths feed at different niches in the “supermarket” of mudflat creatures. The Long-Billed Curlew in particular loves to feast on the ghost shrimp that were abundant in Mission Bay. Sandpipers, plovers, and avocets were abundant, along with the wading Black-necked Stilts. The American Coot looks like a black duck but is a distinct bird that makes its nest among the Cordgrass at water’s edge. Brown Pelicans, Cormorants, Loons, California Gulls, and Western Grebes were also common to Mission Bay waters.

The abundance of game—on land, flying in from the skies, and in the sea—provided an ample diet to the humans living on the shores of Mission Bay. The abundance of wildlife had already diminished after the Spanish implanted the Mission economy, replacing the centuries-long rhythms of human and nature with cattle and the European grasses that came with them. Aquatic life in the Bay continued to thrive in the times before industrial methods were applied to fishing and agriculture. The Native Americans had seals, sea-lions, and sea-otters as part of their culinary options, but the European fur and hide traders had other plans. By the 1830s the sea-otter population, once thought to be as many as 20,000, had plunged. There were only fourteen sea-otters left at Point Sur at the beginning of the 20th century, and it was thought they had gone extinct until a colony of about 100 was “re-discovered” in 1938 during construction of Highway 1 along the coast.

The Salt-Marsh Harvest Mouse is an endangered species that once lived in the hundreds of miles of saltmarshes ringing the bay, including Mission Bay, and is hanging on in the 21st century in some areas of the southern and northern Bay Area. It is a nocturnal creature that builds its nests in the vegetation of the marsh. Certainly it was ubiquitous in the pre-contact era, but loss of habitat has taken a huge toll.

When considering the “natural history” of Mission Bay, we can’t leave out the centuries-long symbiotic relationship that humans had nurtured with the game, fish, and birds that frequented it. Before the arrival of Europeans, a simple but amazingly abundant life ebbed and flowed with the rhythms of the seasons around the San Francisco Bay, and the small human communities that frequented Mission Bay were part of that larger organic system of life. But that natural history gradually disappeared with the arrival of Europeans and eventually urbanization. For decades Mission Bay was a dumping ground for the organic and industrial waste of the new city: the offal from early slaughterhouses along Mission Creek, the raw sewage that poured in from houses and buildings that sat near its original shoreline, and the debris and waste from shipbuilding, power plants, and factories. Just as importantly, we can’t overlook the industrial exploitation of whales that reached its high point (or low point, depending on your perspective) in the late 19th century just a short distance south of Long Bridge, which was by then spanning the mouth of Mission Bay.

The return of dozens of bird and aquatic species to the restored banks of Mission Creek is a powerful demonstration of the resilience of natural processes. After a century and a half of destruction and exploitation, a new ethic of appreciation and cohabitation has spawned a human community dedicated to re-creating habitat and preserving space for non-human species. We can only hope that the small beginnings of this process at Mission Bay will inform and accompany the larger process of transformation taking place throughout the city of San Francisco, and around the Bay and even the world!

This is chapter eighteen of "Vanished Waters: A History of San Francisco's Mission Bay" published by the Mission Creek Conservancy, and republished here with their permission.


125. See Charles C. Mann’s 1491: New Revelations of the Americas Before Columbus (Alfred Knopf, New York: 2005) for a good summary of recent developments.
126. N.C. Nelson, “Shellmounds of the San Francisco Bay Region,” University of California Publications in American Archaeology and Ethnology, Vol 7. No. 4 (The University Press, Berkeley: December 1909), 316.
127.,_1891 accessed June 12, 2010. In 1850 a thirty-three-year-old German physician and naturalist landed in San Francisco to find his fortune. After years of traveling around the world, Hans Herman Behr settled down to a successful medical practice in San Francisco, finding fame as a chronicler of the city’s natural wealth and as an early member of the California Academy of Sciences. He devoted much of his natural history work to insects, primarily butterflies, but he also chronicled the rapid transformation of San Francisco’s flora as the city expanded and its population exploded. Behr later recalled those changes in two short essays entitled Botanical Reminiscences published in 1891 and 1896. One striking feature described by Behr is the extensive freshwater bog near Seventh and Harrison that was later developed as the Russ Gardens.
128. Here are the plants with their latin names in parentheses: large-flowered dogwood (Cornus nuttallii), buckbean (Menyanthes trifoliate), stream orchids (Epipactis gigantean), the white-flowered bog orchid (Habenaria leucostachys (=Platanthera leucostachys), and cotton grass (Eriophorum gracile), leather grape-fern (Botrychium ternatum), lady fern (Asplenium filix-femina var. cyclosorum).
129. More Latin names: Spotted Water Hemlock ( Cicuta californica), Evening Primrose (Oenathera californica), Water Pennywort (Hydrocotyle), Pond Lily (Nuphar polysepalum), and Cattails (Typha latifolia). California Wax Myrtle (Myrica californica), Blueblossom Ceanothus (Ceanothus thyrsiflorus), Coast Silktassel (Garrya elliptica, Salix sp.), Chain Fern (Woodwardia radicans), Asplenium filix-femina, Aspidium aculeatum, and Aspidium munitum; Douglas Baccharis (Baccharis douglasii), Philadelphia Fleabane (Erigeron philadelphicus), local Asters (Aster chamissonis), and Rosilla (Helenium puberulum), flowering Twin-berry (Lonicera involucrate), Elderberry (Sambucus glauca), wild currents (Ribes glutinosum).
130. More Latin names: sedges (Cyperaceae, especially Scirpus, Carex, and, in one locality, even an Eriophorum). Bog Orchid (Habenaria leucostachys) Buckbean (Menyanthes trifoliate) Stream Orchid (Epipactis gigantean), with Californian Blue-Eyed Grass (Sisyrinchium bellum), salt grass (Distichlis maritime), gumplant (Grindelia robusta), Salt Marsh Bird’s Beak (Cordylanthus maritimus) Seaheath (Frankenia grandifolia), California sea-lavender (Statice limonium var. californica), Monkey Tail (Heliotropium curassavicum).
131. Robert Ryal Miller, Captain Richardson: Mariner, Ranchero, and Founder of San Francisco (La Loma Press, Berkeley: 1995), p. 57.
132. N.C. Nelson, “Shellmounds of the San Francisco Bay Region” op.cit.
133. Latin names for the species in this section: “soft-shelled” clam (Macoma nasuta), “soft-shelled” mussel (Mytilus edulis), Innkeeper (Urechis caupo), Arrow Goby (Clevelandia ios), California Ghost Shrimp (Callianassa affinis), California Horn Shell (Cerithidea californica), Cloudy Bubble Snail (Bulla gouldiana), Channeled Dog Whelk (Nassarius fossatus), Bay Sea Hare or Sea Slug (Navanax inermis).
134. Allan A. Schoenherr, A Natural History of California (University of California Press, Berkeley: 1992.

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