CLF has been raising the alarm about pollution in the Great Bay ecosystem for more than two decades. Photo: CLF
April 15, 2026 (Concord, NH) – Eelgrass – underwater seagrasses that are the foundation of the Great Bay estuary’s ecosystem – has collapsed, marking the most severe ecological decline seen in Great Bay in decades. According to a new study, eelgrass coverage across the estuary fell by 80 percent in a single year, dropping from more than 1,000 acres in 2024 to just 211 acres last year. Within Great Bay itself, the loss was even more dramatic, reaching 98 percent in that same period.
“This is the most significant ecological alarm we’ve seen in Great Bay in decades,” said Melissa Paly, Conservation Law Foundation’s Great Bay-Piscataqua Waterkeeper. “These waters and natural landscapes are part of what makes New Hampshire and the southernmost part of Maine special. Our waterways may still look beautiful, but they are in trouble. Eelgrass supports the fish, birds, and wildlife that are a critical part of our regional economy and identity. We know what’s contributing to this loss, and we can do more to protect the estuary if we choose to.”
Eelgrass is the cornerstone habitat of the estuary, supporting fisheries, providing oxygen, improving water quality, stabilizing sediments, and even storing carbon pollution. Its loss signals a system under serious stress and highlights the urgent need to strengthen protections for water quality and coastal resilience.
The findings show that eelgrass health is more stable in the lower estuary near the mouth of the Piscataqua River. A modest increase in seagrass there compared to recent years may be related to cooler temperatures and clearer water where the estuary meets the ocean, as well as improved water quality since Portsmouth significantly upgraded its wastewater treatment facility at Peirce Island.
The stressors on eelgrass – sediment from rain runoff and increasingly intense storms, excess nutrient pollution from wastewater and stormwater, invasive green crabs and warming water temperatures caused by climate change – have all posed challenges to eelgrass health for years.
The alarming loss of eelgrass is not limited to Great Bay. Massachusetts has seen serious loss of eelgrass in recent years. Casco Bay lost more than 50% of its seagrasses over the course of a four-year period, and a 2026 study revealed steep losses in other parts of the Maine Coast. But the one-year, 80 percent decline in the Great Bay estuary as a whole, and the 98% decline in Great Bay, is unprecedented.
Recovery is still possible. Eelgrass is showing signs of recovery in places like Buzzards Bay, Virginia’s Eastern Shore, and Tampa Bay. Long-term commitment is needed if Great Bay’s eelgrass is to recover. Local, state, and federal leaders can and must implement stronger water quality protections, including better stormwater management and investment in restoration.
CLF has been raising the alarm about pollution in the Great Bay ecosystem for more than two decades. We’ve been fighting for stricter Clean Water Act permits, advocating for more effective ways to address stormwater pollution, and working with eelgrass researchers at local universities and organizations on restoration efforts. Recent declines are a clarion call for action and innovation to protect Great Bay in the face of multiple stressors.
CLF experts are available for further comment.
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