Cal Poly research highlights biological changes within estuary when a primary eelgrass habitat is lost 

SAN LUIS OBISPO — The loss of seagrass habitat caused a dramatic shift in fish species in Morro Bay, according to a recently published paper by Cal Poly researchers. 

Once covered with lush eelgrass meadows and unique fish species, areas of the bay are now home to muddy-seafloor-loving flatfish. 

According to the study, Seagrass meadows were previously common throughout the Morro Bay estuary, “Effects of Estuary-Wide Seagrass Loss on Fish Populations,” which was published this spring in the journal Estuaries and Coasts.


“Seagrass, like the eelgrass in Morro Bay, is important because it supports a range of marine life,” said Jennifer O’Leary, who led the research as a California Sea Grant extension specialist based at Cal Poly. “It’s like the trees in a forest — these underwater plants provide food, structure, and shelter to many of the marine animals that live in the bay.”

O’Leary is now the Western Indian Ocean coordinator for the Wildlife Conservation Society, a New York-based non-governmental organization working to conserve the world’s largest wild places in over a dozen priority regions. 

Underwater seagrass meadows — one of the main habitats in coastal estuaries — represent one of the most biologically productive biomes on the planet. Yet seagrass habitats are being lost at an alarming rate, and their decline now rivals those reported for tropical rainforests, coral reefs, and mangroves.

Loss is usually the symptom of a larger problem. For example, seagrasses are considered “coastal canaries,” and their decline signals important losses to biodiversity and often impacts the communities that depend on them. 

Morro Bay estuary, one of 28 that the U.S. Environmental Protection Agency designated as critical to the economic and environmental health of the nation, has seen a dramatic loss in its seagrass habitat. Once dominated by a common California eelgrass (Zostera marina), seagrass at this site has declined by over 95 percent.

In 2007 the seagrass was found throughout the bay, with abundant underwater meadows on the western edge of the estuary, between the dredged harbor channel and the Sand Spit, stretching south from roughly Morro Bay State Park Marina to the back bay. Over the next ten years, it nearly disappeared, dropping from 344 acres to less than 15 acres in 2017.

Seagrass meadows are a multifaceted habitat that secure sediments with their root systems while providing food, shelter, and nurseries for many types of fish and invertebrates. When seagrass meadows are lost, they are often replaced with a less dynamic, muddy seafloor habitat

O’Leary and colleagues in the new study found that seagrass loss did not result in fewer fish but rather led to changes in the types of fish that live in the bay. The research team saw decreasing numbers of some seagrass-specialist fish species, such as the bay pipefish (Syngnathus leptorhynchus). With long thin bodies and olive-green coloration, bay pipefish adapted to hide among the seagrass blades. 

In contrast, researchers observed an increase in flatfishes like the speckled sanddab (Citharichthys stigmaeus) and staghorn sculpin (Leptocottus armatus). With flat bodies that are ideal for life on the muddy seafloor, they are common residents in California bays and estuaries. These species have moved into Morro Bay’s denuded eelgrass habitats and now make up the majority of fish species present there. 

The loss of eelgrass habitat along the California coast presents a larger problem for species that depend on seagrass, like the bay pipefish. If seagrass doesn’t recover, then the surviving meadows will be further apart and have a more fragmented, or patchy, distribution. This distance and patchiness of habitat may impact specialists, like pipefish, by impairing their ability to move to new habitats in search of food or mates. Over time this community isolation may alter the genetic structure and diversity of the overall pipefish population. 

“The relatively sudden and near complete collapse of eelgrass in Morro Bay has not only changed fish populations, but it has also resulted in substantial changes to estuary physics and geomorphology,” said study co-author Ryan Walter, a Cal Poly physics professor who has been studying eelgrass loss through a California Sea Grant-funded research project that launched in 2018.

Walter, O’Leary, and other Cal Poly researchers, in conjunction with the Morro Bay National Estuary Program, continue to study the cause and consequences of the eelgrass decline. In another study published last September, the team found that the loss of eelgrass in Morro Bay led to widespread erosion or sediment loss throughout the estuary.   

The new research published in March sheds additional light on changes within the estuary that may inform how scientists learn about seagrass communities throughout the Golden State. There has not been an eelgrass decline on the Pacific Coast of this magnitude, making Morro Bay a novel event that may help predict future estuarine change. 

A multifaceted approach to protecting and enhancing the remaining seagrass will be essential, said the researchers.

Scientists remain hopeful as the remaining eelgrass is slowly expanding with protection and local planting initiatives, including successful transplant efforts led by the Morro Bay National Estuary Program. Walter and O’Leary have used drone-based surveys to document natural expansion and recovery of eelgrass in areas where it was lost. The mere 9.4 acres of seagrass left in Morro Bay in 2017 expanded to 36.7 acres by 2019. Researchers are still analyzing data from 2020 but are optimistic that the seagrass acreage continues to increase slowly.