What is an estuary?

What is an Estuary?

An estuary is where freshwater meets the salty sea.

Estuaries form when rain runs off the land through rivers, streams, or groundwater, meets and mixes with saltwater from the ocean, and creates partially enclosed bodies of water along the coast. These environments create more living matter each year than comparably sized areas of forest, grassland, or agricultural land.

Chorro and Los Osos Creeks feed freshwater into Morro Bay, a small estuary of 2300 acres, while a lengthy sandspit protects the area from the Pacific Ocean.

Many animals rely on the sheltered waters of Morro Bay for food, places to breed, and migration stopovers. A lot of the fish our local fishermen catch offshore and we eat at local restaurants spend part of their life in an estuary. Plus, Morro Bay is an important stop-over for migratory birds on the Pacific Flyway, the bird super highway from the Arctic to South America.

Every estuary is different from the next. Habitats can range from the mangroves of Tampa Bay to the swamps of Alabama’s shores to our sandy chaparral communities of Los Osos. Animals found in estuaries include dolphins of Galveston Bay, horseshoe crabs in the Peconic National Estuary, or our growing population of sea otters here in Morro Bay.  While they may not all look the same, estuaries are special places to care for.

The mOrro Bay Estuary

We have created a jurisdictional map of the Morro Bay watershed (linked below and static map pictured below) to help the public learn more about the watershed and land use surrounding the estuary and watershed.



The land that drains to the sea.

A watershed is the area of land where rainfall and groundwater drains into a common outlet, delivering both clean water and land-based pollution. In our Morro Bay watershed, the Nine Sisters, a prominent line of peaks created over millions of years from volcanic activity, divides our Morro Bay watershed into two valleys, Los Osos and Chorro.




The Morro Bay estuary and watershed encompass a range of habitats.  


Maritime chaparral—Older and more stable sand dunes away from the immediate coast. Hosts plants such as buckbrush and chamise.

Coastal scrub—Made of steep slopes, moderately dry, and low overhead canopy. Identified by plants such as black sage and sticky monkeyflower.

Estuary and salt marsh—Tolerant of salty and fresh water conditions and being completely underwater for periods of time. Identified by plants such as pickleweed or western marsh rosemary.

Grasslands—Often turned to farm or grazelands. If the rich soil is left to its own, bunchgrasses often emerge. Identified by plants such as SLO indian paintbrush or Cambria morning glory.

Oak woodlands— Near the shore, it has a thick cover of leaves and branches, while more inland, where the moisture becomes more scarce, overhead cover develops in a more open fashion. Plants beneath the coast live oaks include miner’s lettuce and yerba buena.

Creek corridors—Lines creeks, streams, and rivers with dense vegetation to cool the flowing water. Also helps slow the water flow as well as stabilize the banks to control erosion. Identified by a mixture of overhead trees such as willows or elderberry and low-lying plants such as California blackberry or California honeysuckle.

Sand dunes—Difficult for plants to establish with salt spray, shifting sands, inability for ground to hold water, and constant wind. Identified with sparse communities of plants such as beach morning glory and sand verbena.

These habitats host some plants that can only be found locally, such as the Morro manzanita (Arctostaphylos morroensis) of the maritime chaparral communities. They are also home to some threatened and endangered plants, including sueda Californica and salt marsh bird’s beak.

Check out our Native Flora of Morro Bay guide for more details about local habitats and native plants of Morro Bay.




The Morro Bay estuary and watershed is home to many types of animals.  


In the hills, you can find bobcats hunting in the grassy slopes or California horned lizards sunning themselves along rocky outcrops.

At the creeks, you can see steelhead trout hidden under branches beneath the water and western pond turtles carefully balanced on logs along the stream’s edge.

In the bay, California brown pelicans travel by air in search of fish, southern sea otters float with their pups in the calm waters, and bat rays glide below the surface.

It would be hard to name all of the animals of our area. Instead, we have a guide for particularly sensitive animals and even some more plants of the area. Check out our Atlas of Sensitive Species in Morro Bay guide.

Did you know that the Morro Bay estuary is home to more than a dozen threatened or endangered species? The Morro shoulderband snail (Helminthoglypta walkeriana), Western pond turtle (Actinemys marmorata), California red-legged frog (Rana draytonii), and California black rail (Laterallus jamaicensis coturniculus) are just a few of those species.

We also feature native animals on our weekly blog. Sign up for the articles to be delivered to your email inbox, so you won’t miss the next Wildlife Spotlight.




Tourists and locals alike enjoy boating, biking, paddling, diving, birdwatching, and hiking in and around Morro Bay.


The miles of bay-front trails and protected waters make the bay a great place for all these activities. Use our Estuary Program Map (PDF) to find your way.


Don’t forget that it’s protected!


Morro Bay is a special place that is also a marine protected area. Please take care that you don’t accidentally harm the area or its wildlife on your visit. Check out the links and tips below for more information on marine protected areas and protecting the endangered snowy plover:

Morro Bay SMRMA

Morro Bay SMR

Protecting the Snowy Plover (PDF)

  • Keep a respectful distance from wildlife when walking on the shore and boating. Use binoculars for observation.
  • Don’t allow your dogs to chase birds and wildlife and make sure you pick up their waste.
  • Pack it in, pack it out – be sure to take any trash with you and dispose of it properly.
  • Be sure you understand and adhere to all the rules and fishing regulations for the bay.