Could Shellfish Clean Up San Diego’s Mission Bay?

Oyster Bay, Washington State. Photo Credit: John Rowley, Taylor Shellfish Farms

Oyster Bay, Washington State. Photo Credit: Jon Rowley, Taylor Shellfish Farms

There’s a great irony to the connection between clean water and bivalve shellfish – oysters, mussels and clams in particular – they can only be safely eaten if they’re harvested from clean water. Chic raw bars are popping up in cities like Seattle, San Francisco and New York, but the oysters served on the half shell in waterfront restaurants don’t come from local bays. In all likelihood, they never will – shellfish, like most agricultural products, are grown and harvested in rural areas far from population centers.

Yet shellfish have proven to be a useful tool for water quality remediation in polluted bays along our coastlines. Unlike raising cows, planting wheat or growing lettuce, cultivating bivalve shellfish has environmental benefits: removing excess algae from the water, improving water clarity, supporting eelgrass beds and providing habitat for diverse ecosystems.

New York City and Oyster Restoration

New York City is leading the way in utilizing shellfish to improve local water quality. The New York Harbor Foundation has launched an exciting and ambitious project called the Billion Oyster Project in the former “Oyster Capitol of the World”. This project was developed to restore New York Harbor’s marine ecosystem and to provide educational opportunities for local middle and high school students. Other organizations and companies are pursuing initiatives as well, such as the New York/New Jersey Baykeepers, an ecological advocacy NGO.

A Vision of a Revitalized New York Harbor (SCAPE / LANDSCAPE ARCHITECTURE PLLC)

A Vision of a Revitalized New York Harbor (SCAPE / LANDSCAPE ARCHITECTURE PLLC)

Especially after the devastating impacts of Hurricane Katrina, the idea of restoring oyster reefs into New York Harbor gained traction. The New York Times in particular has repeatedly reported on the mitigating potential of oysters to absorb the wave energy of storms like Hurricane Katrina. Oysters grow generationally in reef like structures, with the living generation on top of the reef. New York Harbor has supported natural oyster reefs in the past, and only lost them because of over-harvesting and pollution. Oysters can’t be grown everywhere, but they can be grown in New York Harbor – it’s been done before.

San Diego

I’m a newcomer to San Diego, but in just a few months, I’ve picked up on a few things. First, local residents are prideful about our coastline; a number of environmental advocacy organizations work on coastline conservation issues. Unlike New York Harbor, San Diegans spend a lot of time in the water. Second, the US Navy and maritime heritage and technology are a deeply embedded and important part of the area’s culture. Third and finally, San Diego and its residents are open to new ideas. San Diego is home to the largest naval base in the Pacific, the largest desalination plant in the country and a booming maritime technology industry.

San Diego is also home to one of the West Coast’s largest aquatic parks: Sea World. Mission Bay in particular is an area of concern for local residents and the City of San Diego. Mission Bay is listed as an impaired body of water due to high levels of coliform bacteria, caused by urban runoff and exacerbated by limited exchange with the Pacific Ocean. Not only can shellfish from the saltwater lagoon not be consumed safely, but the public’s use of the bay for recreational activities is at times limited.

Shellfish are not just used for restoration, as in New York Harbor. In Washington State’s Puget Sound, NGOs like the Pacific Shellfish Institute have experimented with cultivating mussels in working waterfronts with similar water quality challenges. Unlike oysters, mussels are grown suspended in the water column. This method allows them to be grown where they are needed, such as sources of freshwater bringing excess nutrients and waste into the bay.

Mussels, like oysters, filter water to consume algae. Some species of mussels prefer the strong currents and high salinity of the ocean, while others prefer the calmer and more brackish water found in places like Puget Sound and Mission Bay. Mussels would grow well in Mission Bay, and they would certainly have a positive impact on the health of the bay.


Using shellfish for water quality mitigation is not an industry standard practice, and still needs research and experimentation in order to use it as a strategy of scale. In the case of Mission Bay, an organization like Hubbs-SeaWorld Research Institute would be an intriguing partner. As the research arm of SeaWorld, they have a vested interest in Mission Bay; they also are pursuing large-scale commercial aquaculture ventures in partnership with Rose Canyon Fisheries offshore of San Diego’s coast, and using aquaculture for environmental remediation is a complementary practice to commercial aquaculture.

Don Kent, president of Hubbs-SeaWorld Research Institute, stand next to tanks holding yellowtail. The institute is working on a proposal for an open-ocean fish farm in the ocean off San Diego. | Photo Credit: Photo by K.C. Alfred/UT San Diego/Copyright 2015

Don Kent, president of Hubbs-SeaWorld Research Institute, stand next to tanks holding yellowtail. The institute is working on a proposal for an open-ocean fish farm in the ocean off San Diego. | Photo Credit: Photo by K.C. Alfred/UT San Diego/Copyright 2015

One of the primary limiting factors may be access to shellfish “seed”, which are reared in hatcheries. There is more demand than supply for shellfish larvae, and an institution like Hubbs would likely have to either partner with an existing hatchery or expand their own operations. Funding is another limiting factor, but the aquaculture industry and government entities have proven to be willing funders of this type of work. Finally, permitting may be a significant challenge, and is also the biggest unknown. This type of project would require a public/private partnership between the City of San Diego, State of California and SeaWorld. Particularly at the state level, there has been hesitancy to award usage permits for aquaculture ventures. However, as a non-commercial venture, this project may gain traction with state permitters, whose directive is environmental resources management. Finally, an issue that has been a sticking point in the past has been restricting access to the shellfish installations, which would not be deemed safe for consumption. San Diego’s waterfront is owned and managed by a diverse set of organizations, from the US Navy to the State of California and private entities. It would be critical for public access to be restricted, and partnering the with the Navy or private entities would be prudent.

While you likely won’t be able to see the bay where your oysters came from as you’re slurping them down on your city’s waterfront, why not let shellfish clean up the bay instead? Let’s slurp our oysters and let them filter, too.

Correction: This article was corrected to clarify that SeaWorld is not the biggest polluter in Mission Bay. However, there have been accusations made against SeaWorld that are noteworthy, including repeated violations of the company’s discharge permits.

Update: Since writing this article, I’ve become aware of existing efforts to use shellfish for bioremediation in San Diego, including plans for Mission Bay. I’ve also learned about upstart shellfish bioremediation projects elsewhere in Southern California.

Update: Since writing this article, I’ve learned that Carlsbad Aquafarms has a small shellfish hatchery, which could be another potential source of seed for a local shellfish bioremediation project.


2 thoughts on “Could Shellfish Clean Up San Diego’s Mission Bay?

  1. Don Kent says:

    I don’t know who authored this article, but it has some glaring misrepresentations, and I think it is irresponsible to publish comments without taking responsibility for them. First, the name is Hubbs-SeaWorld Research Institute, not “Hobbs”. Hobbs is a syndicated cartoon character, and Dr. Carl L. Hubbs was a renowned marine biologist and Professor Emeritus at Scripps Institution of Oceanography. Also, SeaWorld is not a significant polluter of Mission Bay and placing SeaWorld’s name in the same sentence with mention of concerns over coliform bacteria is hugely misleading to the reader. It is my understanding that SeaWorld’s effluent is highly monitored and regulated under an NPDES permit and only enters the Mission Bay after extensive cleaning and sterilization. The water leaving SeaWorld is far cleaner that the water within Mission Bay. As native if San Diego who is trained as a marine scientist with ties to USD, UCSD and SDSU, and as a former member of the Mayor’s Clean Water Task Force, I understand that the coliform bacteria found in Mission Bay is primarily the result of the marine birds and mammals that use Mission Bay as well as the bacteria that flows into the bay from the watersheds feeding Rose Canyon and Tecolote Creeks. The residency of the bacteria is caused by the single point for tidal flushing in and out of the bay entrance channel which prevents an adequate exchange of bay water with that in the open ocean. Please get your facts straight before publishing information about my city.

    Liked by 1 person

    • Hello Don. I was very surprised to see a response to this posting – I did not realize it was public. I’m curious – how did you come across it?

      I looked into your comments about Mission Bay, and I was wrong to indicate that SeaWorld is a major polluter. From what I can tell now, it’s been over a decade since there were issues with pollution from the park.

      I also went through the blog article and made a few corrections to proper names – thank you for pointing that out. In some cases, the publisher I used actually auto corrected Hubbs to Hobbs, it seems.

      In the beginning of your comment, you mentioned there were some glaring representations. If you feel that I misrepresented other facts, please reply and let me know.

      Thank you for your work.


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s