A Letter to the Community from PREP’s Director: State of Eelgrass in 2026

Dear Community,

At the Piscataqua Region Estuaries Partnership (PREP), our work is to ensure clean water, healthy habitats, and resilient communities through a non-regulatory approach. Our work is made possible by close collaboration with 52 cities and towns across our watershed in both New Hampshire and Maine. As a National Estuary Program, we’ve partnered with communities to make a difference in reducing nitrogen pollution and improving water quality for everyone who lives, works, and plays in our region. We’re proud of the work these communities have done and our role in supporting them. 

Now we face a challenge that has been underscored by one of our recent eelgrass monitoring reports. Eelgrass (Zostera marina) is the dominant species of seagrass found in the Great Bay Estuary. It grows in underwater meadows, helping to stabilize the seafloor and provide homes for fish and shellfish. It also filters nutrients and sediments, improving water quality. But eelgrass has been in decline for decades across New England, including in our Great Bay Estuary. The Great Bay Estuary starts at the mouth of the Piscataqua River and the coast of Kittery, Maine and moves inland toward Great Bay, a large bay south of Adam’s Point in Durham, New Hampshire (map included below). In 1996, eelgrass peaked in the Great Bay Estuary at 2,900 acres and has been slowly decreasing ever since. 

Because eelgrass is a critical habitat and indicator of water quality, PREP has monitored its presence and health in the Great Bay Estuary for decades. We publish three annual monitoring reports with this information. Like annual doctors’ physicals, these reports inform long-term trends that our local partners can use in their decision making, such as land use planning and wastewater treatment. 

One of our annual monitoring reports is conducted by drone (or aerial) mapping. Our most recent aerial report was published on April 2, 2026. While this report indicates a thriving 67% increase in eelgrass acreage in Portsmouth Harbor (the second most coverage that’s been mapped there since 2007), it also reflects a significant decrease within the inland Great Bay, with 887 acres lost (a 98% decrease). This leaves a total of 211 acres in the entire Great Bay Estuary, with only 22 acres of eelgrass habitat in Great Bay proper.     

It is essential to note that the reports do not provide an analysis of cause and effect on changing conditions. The report simply provides a necessary record of that year’s eelgrass acreage. It often takes decades of data to determine trends.  

Nevertheless, we empathize with the shock and concern our community may feel in reading or hearing about this report. We also know how eager our communities are to learn why this decline has occurred and what should be done about it. Because PREP has years of data, we can offer a big-picture perspective to help understand what might be possible, not just for our ecosystem but for the benefit of people in our region.  

That data tells us many things. Changes in eelgrass acreage result from complex factors. Recovery is long-term work. It is not always linear. Even though eelgrass has declined, other species in the Great Bay Estuary are on stronger recovery paths, like oysters which have rebounded from 1.2 million in 2000 to 7.4 million in 2020. We’re also seeing record numbers of migratory fish passing through Great Bay.  

In addition, eelgrass acreage has often fluctuated in the Great Bay Estuary over the years, with different areas thriving or struggling each year. For example, a wasting disease event in 1988-89 reduced Great Bay proper’s eelgrass coverage from 1,686 to 313 acres, an 81% decrease. In 1990, the eelgrass beds recovered, and coverage rebounded to 2,024 acres, increasing for the following three years. (Historical graph of eelgrass acreage in Great Bay proper provided below.)

We know from the data that there are multiple drivers that influence eelgrass health. Factors include nitrogen, stormwater runoff, temperature, precipitation, light, sediment, as well as legacy impacts (like pollution from decades ago). PREP is deeply committed to working with partners to understand and make sense of this complexity. Later this summer, we will convene a Technical Advisory Committee of experts, municipalities, and partners to investigate the findings of our new report in greater detail. In addition, PREP’s active commitment to eelgrass recovery continues. We are funding and collaborating on critical research with local, regional, and national partners, and we are also spearheading innovative seed-based restoration techniques in Great Bay.  

No one can promise what will happen with eelgrass in our region. But if we continue toward making improvements in water quality, it will have essential benefits for our community as well. We encourage our communities to continue the impactful work of conservation and reducing pollution, in particular stormwater runoff. Better stormwater management helps reduce flooding, improves water quality, and supports natural habitats. Even if eelgrass does not respond immediately or directly, these efforts are important and necessary because they will benefit our communities. Not continuing these efforts will exacerbate our challenges. 

Every day, we work with community partners, researchers, and regional organizations that care deeply about our watershed. We are present in a variety of municipal discussions about ways our communities could approach thoughtful development. We encourage our communities to keep pursuing reductions in stormwater pollution as they manage growth. Green infrastructure, wetland protections, and septic maintenance will help mitigate water pollution problems going forward. 

For over thirty years, I’ve worked in our beloved Great Bay Estuary. Throughout the various successes and challenges, the prevailing motivator for me has been collaboration. Collaboration among municipalities, agencies, researchers, and community partners. It is our region’s greatest strength, and, frankly, we’ve never been stronger and more resilient as a partnership. This is what helps me when we get tough news: that we are a resilient watershed that can rise to the challenge. On behalf of PREP, we are committed to working with all of you on our shared responsibility to protect our waterways.  

Everyone is welcome to participate in these collaborations. I extend an open invitation for PREP to meet with your community. We will come to you, listen to your concerns, and share information, resources, and tools that could support you. Please reach out to me (Kalle.Matso@unh.edu). It’s a privilege to serve this community as we tackle these challenges together. 

Sincerely,

Kalle Matso, PREP Director

Additional Resource:

To support you, PREP has compiled a new question-and-answer style resource of the common questions they’ve been asked. Maybe they’re ones you’ve been asking yourself. Or maybe you are looking for simple ways to answer questions posed by your community.

PREP continues to extend an open invitation to meet with your community. Please reach out to PREP Director Kalle Matso (Kalle.Matso@unh.edu) to start the conversation.