Natural Resources & Wildlife

The Port of San Diego is actively involved with protecting San Diego Bay's Natural Resources. Some of these resources include salt marsh and tidal flats, bird nesting and foraging sites, essential fish habitats such as eelgrass beds, and nine federal and state listed endangered or threatened species. Our participation involves the promotion of ecologically minded development decisions, furthering public awareness, the management of sensitive habitats and invasive species and support of related scientific research.

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Natural Resources Management Plan

In 2007, the Port and the U.S. Navy embarked on updating the 2002 Integrated Natural Resources Management Plan.  The management plan was revised and edited by a technical advisory committed.  The committee consisted of different agencies and non-governmental organizations including the Regional Water Quality Control Board, Fish and Wildlife Services, National Marine Fisheries Service, Army Corps of Engineers, U.S. National Park Service, Fish and Game, Audubon Society, State Lands Commission and California Coastal Commission. 

The management plan was recently updated and the final document is available here:

In September of 2000, the Port and the US Navy Southwest Division prepared a Natural Resource Management Plan for San Diego Bay. The plan is a guide to assist the users of the Bay to make better, more cost-effective decisions about the development, conservation, restoration and management of San Diego Bay. The management plan also catalogues the plant and animal species around the bay and identifies habitat types. The plan was awarded the 2001 Partnership Award by Coastal America and an updated version of the plan is in development.

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Invasive Species

The invasion of non-native, or invasive species poses a serious threat to San Diego Bay's ecosystem. Invasive species are those that evolved elsewhere and whose introduction has or is likely to cause harm to the environment, the economy, or human health. Invasive species have arrived in San Diego Bay from all over the world, by intentional and accidental means. They are transported in the ballast water of international ships, arrive attached to boat hulls, introduced intentionally for fishery or mariculture, released as unwanted organisms by aquarists, or spread naturally through dispersal. The first introduction of invasive marine species into San Diego Bay may have come from the ships used by the early Spanish explorers. Some invasive species have been in their current ecosystem for so long that they were assumed to be natives until recent genetic analyses proved otherwise.


Invasive organisms can significantly change the structure and function of an ecosystem. Once introduced, they often grow and spread rapidly because they lack local predators and usually affect native species by competing for food and habitat space.

According to a 1999 study, the following invasive species are present in San Diego Bay: one species of marine algae, one marine protozoan, 47 marine invertebrates, and five marine fish. There are also 28 species of invasive coastal plants. In total, at least 82 non-native species are found in the Bay. This number is not as alarming when compared San Francisco Bay, which is often thought of as the most invaded ecosystem in the world, with at least 234 non-natives and a new species arriving every 12 weeks.

For a complete listing of the invasive species found in and around San Diego Bay, please see Table 2-26 of the San Diego Bay Integrated Natural Resources Management Plan.


Caulerpa taxifolia
Caulerpa taxifoliaAlthough not yet found in the San Diego Bay, Caulerpa taxifolia has a devastating potential. The marine seaweed Caulerpa taxifolia, also known as "killer algae," poses no threat to human health, but it could have devastating ecological and economic consequences for California if it is allowed to become permanently established. This non-native seaweed threatens California's coastal marine life by overgrowing and eliminating native seaweeds, seagrasses, reefs, and other communities. An overgrowth of this species in the Mediterranean is reported to have harmed tourism, devastated recreational diving, and had a costly impact on commercial fishing by altering the distribution of fish and inhibiting the establishment of juveniles. Historically, this species has been used as a popular aquarium plant in peoples' homes, and biologists believe that the Mediterranean outbreak may have been the result of irresponsible aquarium cleaning practices.

Caulerpa taxifolia has a brilliant (almost fluorescent) green color and grows in the form of flat, leafy (fern-like) fronds that extend upward from each main stem. Each stem can grow to nine feet in length and have up to 200 fronds. This algae can be found as individual plants or in dense blankets that may cover many acres. Do not be deceived by its attractive appearance!

If you're an aquarium enthusist, here are some tips for preventing a Caulerpa taxifolia invasion:

  1. If you see this seaweed for sale for your aquarium in a pet store, do not use it!
  2. Do not release any water, plants, or animals from a saltwater aquarium into a street, storm drain, creek, bay, lagoon, or the ocean.
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Natural Resources Surveys Show Port Progress

The Port and U.S. Navy have been working cooperatively to fund studies of the natural resources of San Diego Bay.  In 2011, a bay-wide eelgrass survey and a bay-wide fish survey were completed.  During 2009, Vantuna Research Group completed a  bay-wide fisheries inventory and utilization survey  and in 2012,Vantuna Research Group completed a new bay-wide fisheries inventory and utilitzation survey.  In 2006-07 the first bay-wide avian species survey was conducted and the report was just finalized.  A new bay-wide avian species survey started in March 2009 was completed in December 2010.

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Endangered Eastern Pacific Green Sea Turtles

The Eastern Pacific green sea turtle is a resident of the San Diego Bay. The sea turtles migrate from nesting sites in Mexico, in order to forage in the eelgrass beds in the Bay. A small group of 30 to 60 sea turtles are estimated to reside generally in South San Diego Bay. Years of intensive poaching and harvesting of the turtle have attributed to the sharp decline in the population. San Diego Bay provides a protected foraging habitat for the sea turtles and offers a prime study area for researchers.

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California Least Tern Updates and Photos

This ongoing program includes the implementation of controlling access to nesting sites; site preparation and vegetation control; predator control, ant predator control; public information programs, and monitoring programs. Nesting sites on Port tidelands include the D Street Fill, Chula Vista Wildlife Reserve, and the South Bay Salt Works. The San Diego County Regional Airport Authority manages San Diego International Airport and the Chula Vista Wildlife Reserve.

Some of these pictures of least tern chicks were taken at the San Diego International Airport by Mayela Padilla. The hands belong to Robert Patton, a biologist employed by the Zoological Society of San Diego. He is the only one allowed to handle the chicks.

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In its role as environmental steward of the tidelands around San Diego Bay and a swath of oceanfront in Imperial Beach, the Port oversees a number of species and wildlife preservation programs. One of the most successful programs is the protection of the endangered California least tern (Sterna antillarum browni). Historically, the nesting site at the Port’s wildlife reserve areas in Chula Vista has had one of the highest percentages of surviving fledglings in San Diego County.

“We attribute the higher productivity to the enhanced habitat quality on the east side of San Diego Bay,” said Robert Patton, consulting biologist with the San Diego Zoological Society. The Port has contracted with the Zoological Society since 1997 to monitor and provide protection for the endangered California least tern.

Around April every year, the birds arrive at their ancestral nesting areas in Southern California, which includes the Port’s wildlife reserve areas in Chula Vista. Favored tidelands nesting sites for these migrating birds include the Chula Vista Wildlife Reserve and the Sweetwater Marsh National Wildlife Refuge. Nests are small depressions scraped in the beach sand. The females lay one to three well-camouflaged eggs. Robert Patton and his team of biologists visit these nesting sites twice a week to count eggs and band hatched chicks. Newborn chicks fledge quickly and are able to fly in a few weeks. To boost the survival rates of the vulnerable chicks until they fledge, staff from Wildlife Services and UC Riverside keep a close eye on predators in the area.

Many environmental projects that have been funded by the Port, such as restoration of eelgrass and storm water runoff controls, have boosted the survival rate of the young terns by providing cleaner bay water and abundant fish species for feeding the chicks.

“The least tern nest numbers and pair numbers have generally increased on Port tidelands over the years,” said Patton. “We consider the Port’s least tern program a success.”

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