3 Estuaries

Saving the Bay – San Francisco Bay: A Unique Estuary

San Francisco Bay is a unique, biologically productive estuary due to its size, scope and Mediterranean climate.


Is there life deep in the ocean?

Yes, there is life even at great depths in the ocean. One example of deep ocean life is this deep-sea chimaera. Chimaeras are related to sharks and resemble them somewhat. But most chimaeras are adapted for life thousands of feet under the ocean surface. This is one example of an organism that lives in an aquatic biome.

Aquatic Biomes

Recall that terrestrial biomes are defined by their climate. That’s because plants and animals are adapted for certain amounts of temperature and moisture. However, would aquatic biomes be classified in the same way? No, that wouldn’t make much sense—all parts of an aquatic environment have plenty of water. Aquatic biomes can be generally classified based on the amount of salt in the water. Freshwater biomes have less than 1% salt and are typical of ponds and lakes, streams and rivers, and wetlands. Marine biomes have more salt and are characteristic of the oceans, coral reefs, and estuaries.

Most aquatic organisms do not have to deal with extremes of temperature or moisture. Instead, their main limiting factors are the availability of sunlight and the concentration of dissolved oxygen and nutrients in the water.

Marine Biomes

Aquatic biomes in the ocean are called marine biomes. Organisms that live in marine biomes must be adapted to the salt in the water. For example, many have organs for excreting excess salt. Marine biomes include the oceans, coral reefs, and estuaries (Figure below). The oceans are the largest of all the ecosystems. They can be divided into four separate zones based on the amount of sunlight. Ocean zones are also divided based on their depth and their distance from land. Each zone has a great diversity of species. Within a coral reef, the dominant organisms are corals. Corals consist partially of algae, which provide nutrients via photosynthesis. Corals also extend tentacles to obtain plankton from the water. Coral reefs include several species of microorganisms, invertebrates, fishes, sea urchins, octopuses, and sea stars. Estuaries are areas where freshwater streams or rivers merge with the ocean.

An example of a marine biome, a Northern Bull Kelp (Nereocystis leutkeana) forest, from the Northeast Pacific Ocean.

Freshwater Biomes

Freshwater biomes are defined by their low salt concentration, usually less than 1%. Plants and animals in freshwater regions are adjusted to the low salt content and would not be able to survive in areas of high salt concentration, such as the ocean. There are different types of freshwater biomes: ponds and lakes (Figure below), streams and rivers, and wetlands. Ponds and lakes range in size from just a few square meters to thousands of square kilometers. Streams and rivers are bodies of flowing water moving in one direction. They can be found everywhere. They get their starts at headwaters, which may be springs, melting snow, or even lakes, and then travel all the way to their mouths, emptying into another water channel or the ocean. Wetlands are areas of standing water that support aquatic plants. Wetlands include marshes, swamps, and bogs.

Lake Tahoe in Northern California is a freshwater biome.

Aquatic Biomes and Sunlight

In large bodies of water, such as the ocean and lakes, the water can be divided into zones based on the amount of sunlight it receives:

  1. The photic zone extends to a maximum depth of 200 meters (656 feet) below the surface of the water. This is where enough sunlight penetrates for photosynthesis to occur. Algae and other photosynthetic organisms can make food and support food webs.
  2. The aphotic zone is water deeper than 200 meters. This is where too little sunlight penetrates for photosynthesis to occur. As a result, producers must make “food” bychemosynthesis, or the food must drift down from the water above.

Aquatic Biomes and Dissolved Substances

Water in lakes and the ocean also varies in the amount of dissolved oxygen and nutrients it contains:

  1. Water near the surface of lakes and the ocean usually has more dissolved oxygen than does deeper water. This is because surface water absorbs oxygen from the air above it.
  2. Water near shore generally has more dissolved nutrients than water farther from shore. This is because most nutrients enter the water from land. They are carried by runoff, streams, and rivers that empty into a body of water.
  3. Water near the bottom of lakes and the ocean may contain more nutrients than water closer to the surface. When aquatic organisms die, they sink to the bottom. Decomposers near the bottom of the water break down the dead organisms and release their nutrients back into the water.


  • aphotic zone: Area in aquatic biomes deeper than 200 meters so little light penetrates the water.
  • aquatic biome: Biome that is based in the water, such as ponds, lakes, streams, or oceans.
  • chemosynthesis: Process of using the energy in chemical compounds to make food; characteristic of producers in ecosystems without sunlight.
  • coral: Marine animals typically living in compact colonies of many identical individual “polyps”; includes the reef builders that inhabit tropical oceans and secrete calcium carbonate to form a hard skeleton.
  • coral reef: Underwater structures made from calcium carbonate secreted by corals; colonies of tiny living animals found in marine waters that contain few nutrients.
  • estuary: Partially enclosed body of water where freshwater from rivers and streams meets and mixes with salt water from an ocean.
  • freshwater biome: Aquatic biome with a slat content of less than 1%; ponds and lakes, streams and rivers, and wetlands.
  • headwaters: Source of a river or stream; the place where a river begins its journey.
  • marine biome: Aquatic biome in the salt water of the ocean; also includes coral reefs and estuaries.
  • mouth: Part of the river where it empties into another body of water, such as another river, lake, bay, or ocean.
  • photic zone: Area in an aquatic biome that extends to a maximum depth of 200 meters so that at least some light penetrates the water.
  • photosynthesis: Process by which specific organisms (including all plants) use the sun’s energy to make their own food from carbon dioxide and water; process that converts the energy of the sun, or solar energy, into carbohydrates, a type of chemical energy.
  • wetland: Land area that is saturated with water, either permanently or seasonally, with the characteristics of a distinct ecosystem.


  • Aquatic biomes are distinguished by the availability of sunlight and the concentration of dissolved oxygen and nutrients in the water.
  • The photic zone extends to a maximum depth of 200 meters, while the aphotic zone is deeper than 200 meters.
  • Aquatic biomes in the ocean are called marine biomes.


Use the resources below to answer the questions that follow.

  1. What factors determines the distribution of life in lakes?
  2. What is a main entry point for nutrients in the littoral zone in lakes? How does this affect the biomass of this zone? How does it affect the species diversity?
  1. What factors combine to create a wetlands?
  2. What effect do wetlands have on water quality? How does this work? How do you think this process affects biodiversity of wetlands? Be as specific as you can.
  3. What is an estuary? How and why does the salinity of estuaries vary? How does this affect the organisms living in estuaries?


  1. Aquatic biomes are defined by what factors?
  2. How is life in the aphotic zone different than the photic zone?

What may be the most biologically diverse type of ecosystem?

These are wetland marshes in Delaware. Notice the abundance of vegetation mixed with the water. And of course, where there are plants, there are animals. Wetlands are considered the most biologically diverse of all ecosystems. Plant life found in wetlands includes mangrove, water lilies, cattails, black spruce, cypress, and many others. Animal life includes many different amphibians, reptiles, birds, insects, and mammals.

Freshwater Biomes

Freshwater biomes have water that contains little or no salt. They include standing and running freshwater biomes. Standing freshwater biomes include ponds and lakes. Lakes are generally bigger and deeper than ponds. Some of the water in lakes is in the aphotic zone, where there is too little sunlight for photosynthesis. Plankton and plants, such as the duckweed in Figure below, are the primary producers in standing freshwater biomes.

Duckweed and cattails are respectively the primary producers in standing and running freshwater biomes

The pond on the left has a thick mat of duckweed plants. They cover the surface of the water and use sunlight for photosynthesis. The cattails on the right grow along a stream bed. They have tough, slender leaves that can withstand moving water.

Running freshwater biomes include streams and rivers. Rivers are usually larger than streams. Streams may start with runoff or water seeping out of a spring. The water runs downhill and joins other running water to become a stream. A stream may flow into a river that empties into a lake or the ocean. Running water is better able to dissolve oxygen and nutrients than standing water. However, the moving water is a challenge to many living things. Algae and plants, such as the cattails in Figure above, are the primary producers in running water biomes.


wetland is an area that is saturated with water or covered by water for at least one season of the year. The water may be freshwater or salt water. Wetlands are extremely important biomes for several reasons:

  • They store excess water from floods.
  • They slow down runoff and help prevent erosion.
  • They remove excess nutrients from runoff before it empties into rivers or lakes.
  • They provide a unique habitat that certain communities of plants need to survive.
  • They provide a safe, lush habitat for many species of animals, so they have high biodiversity.

See Biomes: Wetlands at http://www.neok12.com/php/watch.php?v=zX03547a4151505c53040173&t=Ecosystems and Biomes: Freshwater athttp://www.neok12.com/php/watch.php?v=zX466d047304046105745367&t=Ecosystems for additional information.

KQED: Restoring Wetlands

More than 100,000 acres of wetlands are being restored in the Northern California Bay Area, but how exactly do we know what to restore them to? Historical ecologists are recreating San Francisco Bay wetlands that existed decades ago. To learn more, seehttp://science.kqed.org/quest/video/wetlands-time-machine/.

For more than 100 years, south San Francisco Bay has been a center for industrial salt production. Now federal and state biologists are working to restore the ponds to healthy wetlands for fish and other wildlife. Salt marshes are rich habitats that provide shelter and food for many species, some of which are endangered or threatened. Seehttp://www.kqed.org/quest/television/from-salt-ponds-to-wetlands for additional information.

KQED: San Francisco Bay: A Unique Estuary

An estuary is a partly enclosed coastal body of water with one or more rivers or streams flowing into it, and with a free connection to the ocean. Estuaries can be thought of as the most biologically productive regions on Earth, with very high biodiversity. Estuaries are zones where land and sea come together, and where fresh and salt water meet.

The San Francisco Bay is one of the great estuaries of the world. Seehttp://www.youtube.com/watch?v=clZz2OjE5n0&playnext=1&list=PL0AAA2B9B3E9F6AB3 for further information.


  • Freshwater biomes include standing water and running water biomes.
  • Wetlands are extremely important biomes. They may have freshwater or salt water.


Use this resource to answer the questions that follow.

  1. Why are freshwater biomes considered “limited”?
  2. Describe a wetland. Give examples of wetlands.
  3. What are the 3 zones of ponds and lakes?
  4. Compare the littoral zone to the profundal zone.
  5. What types of organisms can thrive in the headwaters of streams and rivers?
  6. Describe the changes that occur when a river empties into a lake or ocean.


1. Describe a freshwater biome.

2. Define a wetland.

3. A developer wants to extend a golf course into a wetland. Outline environmental arguments you could make against this plan.



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