The Tijuana River Estuary: A living laboratory

A snowy egret walks among green plants in low water.

(William Bay/TRNERR)

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Just south of San Diego, is Southern California’s largest coastal wetland, the Tijuana River National Estuarine Research Reserve (TRNERR). Nestled next to the cities of Tijuana, Imperial Beach, and San Diego, the reserve boasts 2,500 acres of beach, dune, mudflat, salt marsh, riparian, coastal sage scrub, and upland habitats.

Dusk at the Reserve. (William Bay/TRNERR)

This estuary is fed by the Tijuana River Watershed, which covers 1,750 square miles of Mexico and Southern California. It is home to hundreds of native species, including birds such as loons, egrets, herons, and osprey, as well as many fish and reptile species, coyotes, bats, and even some small shark species such as the leopard shark. Estuaries are living laboratories, rich in biodiversity and invaluable information. This reserve, and ones like it, are ecologic and geologic treasures, vital to biological health. They provide unique habitats, natural water filtration, and can be useful indicators of climate change. 

Introducing Jeff Crooks

Even though I have lived in San Diego off and on since I was a child, I never knew that this gorgeous Reserve existed until recently. Once I heard about it, I knew I needed to learn more about it and the wonderful work that they do there. To do so, I reached out to Jeff Crooks. 

Jeff Crooks, and Marya Ahmad from California State Parks work together on vegetation sampling. On assignment for Southwest Wetlands Interpretive Association & Tijuana River National Estuarine Research Reserve. For usage requests, please contact me, or visit

Since 2002, Crooks has been the research coordinator at TRNERR. Crooks received his Ph.D. from the Scripps Institution of Oceanography, University of California San Diego. He was also a Postdoctoral Fellow at the Smithsonian Environmental Research Center in Maryland and San Francisco. Crooks runs the Reserve’s research and monitoring program started by the NOAA NERR (National Estuarian Research Reserves). It is known as the System-Wide Monitoring Program or SWMP. Founded in 1996, it is now one of the longest running programs of its kind.  The goal of the project is to monitor the short-term variability and the long-term changes in the estuary. This includes monitoring weather, plants, animals, temperature, salinity and dissolved oxygen levels. These are invaluable indicators for the overall health of the estuary and surrounding areas.

What is an estuary?

Estuaries have two main functions, said Crooks. They filter water that flows from watersheds into the ocean, and they are habitats for hundreds of species. Estuaries are found on the border of coastlines, where freshwater rivers and streams meet the ocean. Freshwater flows through the watershed, picking up sediment and pollution. It then deposits into the estuary and becomes brackish water, salty but not as salty as ocean water. This is where the water is filtered via plants, and where extra sediment is collected. Eventually, the filtered water joins the ocean, and the process is complete. According to Crooks, one of the major services of an estuary is creating Blue Carbon, which is carbon that has been sequestered by plants and soil but will never be released back into the atmosphere. This is due to the constant moisture and aquatic plants that are far too wet to burn. Unlike forests or grasslands that burn easily, marine plant matter is fire resistant. 

Estuaries are also ecological goldmines. They are nesting grounds for birds and fish, and they are home to hundreds of plants, sharks, rays and skates, invertebrates, and benthic animals such as muscles and barnacles. Estuaries provide a safe harbor for migrating birds and breeding grounds for many of these species. They also act as coastline nurseries, safe and protected from ocean storms. 

What are the threats to estuarine life?

Unfortunately, this rich and biodiverse habitat is under threat from a variety of modern day challenges. According to Crooks, during the rainy season, there can be 20-25 million gallons a day of stormwater entering the estuary. This stormwater is a mix of sediment, water, untreated sewage, garbage, and street and farm runoff. The damage that stormwater pollution has on biodiversity has the potential to be lethal. Two of the most hazardous chemicals found in runoff are nitrates and phosphorus. These chemicals are found heavily in farm and city runoff, from waste and fertilizers. The introduction of these nutrients to estuaries, oceans, lakes, rivers, etc. can cause Harmful Algal Blooms (HABs), and subsequent dead zones. A dead zone, or Hypoxic Zone, is an area of water where a HAB has occurred. These areas are devoid of nearly all marine life.

 A well-known hypoxic zone is in the Gulf of Mexico. This 6,334 square mile area became hypoxic due to the farm and urban runoff flowing down the Mississippi River and into the gulf. As the nutrients from the runoff enter the watershed, it causes algal blooms. Algal blooms eat up all the oxygen in the water. As the algae eventually decays, it clogs the gills of fish and invertebrates, and chokes corals and aquatic vegetation. These blooms can wipe out entire ecosystems of native and endemic species. And since most algae are invasive, they often out-compete native aquatic plants.  These blooms are incredibly hazardous to all life in the area, including humans. It can take many years for an ecosystem to return to normal after a HAB, and in many cases, it never recovers. 

Crooks also said that one of the other main threats to the estuary is sediment build-up. As stormwater enters the system it carries sediment with it. If the sediment is not filtered successfully, it will build up and smother plants, bird, and fish nests, and will later flow directly into the ocean. This can be hazardous for both human and animal species, as this sediment and stormwater may contain raw sewage. 

The Reserve

At TRNERR, they are dedicated to conserving the estuary and providing education, stewardship, volunteering, and research opportunities. They also value the history of the area by spotlighting the voices of members of the Kumeyaay Nation, San Diego’s Indigenous peoples in the Reserve’s podcast, Divided Together.

So far, episodes of their podcast featured the voices of Kristie Orosco, of the San Pasqual Band of Diegueno Mission Indians; Mike Connolly, of the Campo Band of Diegueno Mission Indians, and Ana Gloria Rodriguez, Kumeyaay from San Jose de la Zorra. Topics on the podcast have included land use practices of Kumeyaay, the repercussions of splitting the Kumeyaay land in two, and the cultural, social, and environmental impacts of the separation that was established in the 1850’s.   

At TRNERR, there are also many fascinating and important research projects. Crooks and I discussed some of the Reserve’s research projects, including their project with UC San Diego, called Cross Surfzone/Inner-shelf Dye Exchange, or CSIDE. Ocean-safe dye was used to test the dispersion rate and direction of ocean water. Researchers placed fluorescent pink dye in the surf zone to determine where the water goes if there are contaminants, invasives, or other forms of pollution. 

Researchers have also released the dye at the mouth of the estuary on three separate days and found that the dye dispersed south, and then out to sea. This indicates that currents take most of the water south and then out, but not north. According to CSIDE, this was a significant discovery, as pollution will follow a consistent dispersion and will mostly flow south towards Mexico. 

This represents a health and safety issue, as the Tijuana beaches to the south are popular tourist locations, and people and animals may be at risk. While most of the stormwater pollution in the area comes from Mexico, it is imperative that the United States works with Mexico to build the necessary infrastructure to mitigate the shared effects of pollution.

Moving forward

TRNERR and the United States government are working with Canada and Mexico to remedy some of the border’s pollution issues. The goal is to build more “gray infrastructure”, structures such as dams, seawalls, roads, pipes, or water treatment plants. This infrastructure will resolve some of the pollution issues, keep the watershed clean, reduce sediment buildup, provide jobs, and help to keep both people and animals healthy.

A Snowy Plover nests in Imperial Beach sand dunes that divide the beach and the Tijuana Estuary. On assignment for Southwest Wetlands Interpretive Association & Tijuana River National Estuarine Research Reserve. For usage requests, please contact me, or visit

As of July 2022, the Environmental Protection Agency, in a joint effort with U.S. International Boundary and Water Commission, drafted their Programmatic Environmental Impact Statement, for the proposed United States-Mexico-Canada Agreement. The proposed action is called the Mitigation of Contaminated Transboundary Flows Project. The project’s goal is to build infrastructure to reduce transboundary flows of untreated wastewater, trash, and sediment. Projects like these are wonderful examples of how we can cooperate and face these challenges together. 

I am so grateful for the work that  Crooks and his team do at the Reserve. Their accomplishments far outnumber what I can include here, so please check out the TRNERR website for information on their Saturday speaker series to learn from estuary experts, go on guided nature walks, or volunteer. There you can also find their podcast Divided Together and learn more about the Tijuana Estuary, as well as the reserve’s educational and research programs. May they continue to protect such a beautiful place and bring awareness to how precious estuaries are.

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