Eelgrass Update: What We Know & Your Questions

Certainly not. Eelgrass can recover and become abundant again, but it will require our continued work for cleaner water. In addition, doing more for clean water will provide other benefits besides helping eelgrass. Stormwater management can help mitigate flooding and support herring habitat, oyster habitat, and salt marshes in addition to helping eelgrass.

Together, we’ve set out some goals for pollution reduction. We’ve made progress, but we haven’t come close to achieving our goals. Why would we stop now? Some people think that because we decreased pollution by some amount, we should see a corresponding gain in eelgrass. That assumes that the system is very simple and responds instantly. That’s not the way it works in the human body nor in a large ecosystem. Things take time.

We have seen some good news in Portsmouth Harbor related to eelgrass. This good news is possibly related to pollution reduction. But there are differences. Portsmouth Harbor has very heavy and coarse sediments similar to beach sand. These coarse sediments will not hold on to past pollution as long as the finer sediments found in Great Bay. Great Bay could take a while to process all the past pollution.

It is not the “baseline” but rather the peak in recent (since 1981) monitoring.

Consistent monitoring of the entire estuary has only been happening since 1999. The first year the whole estuary was monitored was in 1981, and there was over 2,700 acres of eelgrass. The next time the whole estuary was monitored for eelgrass was in 1996 and there was 2,900 acres. Since 1996, the trend shows decreasing eelgrass overall. Sometimes, the record shows a “recovery year,” but that is followed by a decrease again, and the next recovery is not as high as the previous recovery.

In the Great Bay proper, the consistent record began in 1981. From 1981 to 2000, the average acreage was 1,988. In 2022, the acreage was 1,481 and then it fell steeply in 2023 to 855 acres. In 2025, this number shrank to 22 acres.

There are many ways that water can be polluted. In some ways, the water is cleaner since the 70s and 80s. In other ways, it’s not.

We do have less raw sewage than we did in the 70s and 80s, but we have a similar amount of nitrogen going into the estuary due to the increases in human population and wastewater. Between 2003 and 2015 especially, nitrogen loading was much higher—often times more than double—what it was in the 80s.

We also have a lot more impervious surface than we used to have, which means that stormwater travels faster into the estuary. Increasing water temperatures in Great Bay proper (as opposed to Portsmouth Harbor) means that the water has to be clearer to support eelgrass. That's because warmer temperatures speed up the plant’s metabolism and it needs to photosynthesize more.

No. In this case, the loss of eelgrass is related to water in the Great Bay proper (south of Adams Point) not being clear enough to support eelgrass. While this can make things difficult for oysters and fish and other creatures, it’s not a threat to human health directly.

Due to all the great wastewater treatment plant upgrades recently, shellfish harvesting opportunities have increased.

The event in the 1980s was related to a particular disease, called “wasting disease." Wasting disease can sometimes strike healthy eelgrass beds. The steady and slow decrease of eelgrass since 1997 is a very different situation.

In the short term, the fact that we’ve had several bad years in a row does make things more challenging, because there are less seeds to start new grass. But, yes, eelgrass can recover, but it may take several years or more.

While eelgrass has recovered quickly in the past, that was because there were plenty of eelgrass seeds in the sediment. Now that we've had three challenging years in a row, there are much fewer seeds and they are only viable for around a year.

For this reason, we are hoping to restore eelgrass meadows using seeds. This is particularly important for Great Bay proper, which is primarily seed-based. This means new grass comes from a single seed rather than as a new shoot from the root system. In Portsmouth Harbor, however, most of the plants over-winter and come up from root systems.

This is why it’s so important to use these next years to improve water quality. When water quality is better and we have seeds in the system, they have a better chance of surviving.

Pollution, changing weather patterns, and changing land use are factors contributing to this sudden loss. While as a watershed we have reduced pollution, we still have a long way to go. Additionally, we've had consistent rainy spring weather since 2023. These conditions have been very hard on eelgrass in Great Bay proper.

More impervious cover and more frequent storms means more non-point source pollution. Non-point source pollution is runoff that includes nitrogen, phosphosphorus, and sediments. This is going to have an effect.

Yes, we’ve reduced nitrogen from waste water treatment plants, and that’s a great success! But with regard to nitrogen, that’s only 22 percent (22%) of the problem. Seventy-eight percent (78%) comes from non-point sources (like stormwater runoff). So, when we keep having these really rainy springs, that does three things:

1. The water flow itself can stir up the bay. It’s important to slow the water down as much as possible. That’s why we manage stormwater and conserve land.
2. When things get stirred up, past pollution can be brought out of the sediments and into the water column. This is especially an issue Great Bay proper (and not on the coast at Portsmouth Harbor).
3. Rain washes nutrients, sediments, and natural organic matter into the Bay. When that happens, the water becomes cloudy and that blocks light for eelgrass. The fact that this happens is not a huge surprise. However, it is a huge disappointment, given the good work being done.

We knew that the situation in 2025 was concerning, because we have SCUBA divers out in the water monitoring sites from April through October. In the Spring, especially, the water was extremely stirred up. We have been really concerned about eelgrass, especially since 2023. That's when we had a large decrease. When levels get low, you can hit a tipping point when it gets very hard for the habitat to sustain itself. So while we knew this could happen, we hoped it wouldn’t.

We knew that conditions in Great Bay proper had been in a cautionary state. We’ve been sharing those issues more intensely since our 2023 State of Our Estuaries Report. In our report, we used a bubble graphic where each estuary indicator was categorized as either Positive, Cautionary, or Negative. Eelgrass was in the cautionary zone, despite the improvements in Portsmouth Harbor. It was in that cautionary zone because of the Great Bay proper’s eelgrass health decline.

Then, in 2023, storms and rainfall may have exacerbated a fragile environmental situation. Since then, unpredictable extreme weather may have been contributing to worsening conditions. Nevertheless, the scale of the loss in one year (2024-2025) has been surprising and concerning.

That said, having strong regional partnerships allows us to approach difficult questions with shared information and purpose. The collaborative structure we have in place with partners throughout our region makes this work possible. Many partners have made significant investments to reduce nitrogen and improve water quality over the past decade, especially with regard to nitrogen coming from wastewater treatment plants. Those efforts remain essential and valuable to improving conditions in the estuary. The same goes for continuing work work related to non-point source pollution. For example, stormwater management, septic systems improvements, and other management tactics.

We've reduced the nitrogen that's currently going in to the estuary from wastewater treatment plants. That's good. But we know that the nitrogen that went into the estuary before the upgrades is still coming out of the sediments. Also, nitrogen isn't the only problem.

It’s complicated. First, let’s focus on nitrogen, even though it’s not the only stressor of concern. Yes, we have reduced nitrogen from point sources, but that only accounts for 22% of the nitrogen currently going into the estuary. Also, lots of nitrogen from past decades accumulated in the sediments and can slowly come out over time, especially in stormy conditions.

Keep in mind that systems frequently take over 10 years to fully respond to reductions in nitrogen.

When it comes to tributaries that flow into Great Bay proper, we only started reducing treatment plant nitrogen in 2017. That effort began with the Newmarket upgrade.

Secondly, nitrogen isn’t the only stressor. Total suspended solids (TSS) are another factor. TSS can be a mixture of sediments and any piece of organic matter that can’t get through a 0.7 micron filter. Another factor is colored dissolved organic matter (CDOM). CDOM have also increased, and these constituents also reduce light and negatively impact eelgrass.

The trend of increasing rainfall, which adds more nitrogen, TSS, and CDOM to our system, presents a danger to eelgrass. Addressing stormwater issues, conserving open space and restoring habitats will help with these issues.

They’re both important. That’s why we urge communities to better control stormwater and conserve more land.

Experts are still collecting and analyzing data to better understand the relative influence of sediments versus nutrients. There is evidence that this influence is very different for Great Bay proper versus Portsmouth Harbor. In Great Bay, there seems to be more organics floating around with the sediment, which points to the influence of nutrients. In Portsmouth Harbor, the water is clear most of the time. But when it is cloudy, the cloudiness is more due to sediments than nutrients.

No, we don’t.

The EPA Total Nitrogen General Permit put out an “initial threshold” level of nitrogen “loading” that we should aim for. “Loading” means how much nitrogen is going into the estuary. This number was based on studies of many estuaries in New England. Our most recent assessment of “loading” was for 2020. 2020 was a relatively low precipitation year and so the nitrogen loading was lower than previous years.

But still, we would have needed a 44 percent (44%) loading reduction that year to hit EPA’s initial threshold.

So, there’s a lot more work to do. The regulators, PREP (non-regulatory), and municipalities understand this is just an initial target. We need use data to get a more accurate number. This work is currently underway but will probably still take many years, perhaps as many as seven or 10, depending on available funding.

We encourage more focus more on stormwater, septic system improvements, and conservation. These will address the large “non-point source” aspect of the problem.

Communities have already done so much to decrease pollution from waste water treatment plants. Septic systems account for over 20% of the non-point nitrogen load.

In addition, nutrients are not the only stressors on eelgrass. Therefore, point source reductions alone may not resolve the issues eelgrass beds face.

When you conserve land and control stormwater better, you reduce nutrients, total suspended solids, colored dissolved organic matter (CDOM), and other pollutants from entering Great Bay proper (as well as the entire estuary). In some cases, just the water flow itself can stir up the bay, which leads to cloudier water and less light for eelgrass.

PREP engages with many partners including several "external advisors" who have not only studied data on the Great Bay Estuary, but they have also studied many other estuaries as well. The scientific consensus is clear that pollution remains a part of the problem, even though it is not all of the problem. Therefore, putting further actions on hold would not be a good idea for ecosystem health.

Ecoystems are like human bodies, so let’s use a metaphor from human health. If your vital signs were a problem, a doctor might tell you to reduce your food intake by 1000 calories, reduce your stress and exercise more. Let’s then consider that you work really hard and reduce your calorie intake by 300 but not by 1000. While you know that you haven’t reached the goal that was set, you are still hoping for every 100 calories that you decreased, you would see an increase in your vital signs. But that’s not necessarily the case because calories are not the only problem. Plus, you didn’t reach the initial goal that was set by the doctor anyway.

This scenario is very similar to the situation the watershed is in. We have set nitrogen goals but we haven’t actually come close to reaching them yet. Also, there are other stressors that have been particularly challenging the last few years. If we want a healthy watershed, it does not make sense to change direction.

No, we’ve known that stormwater and septic systems were important. On the other hand, the precipitation—especially in the spring—over the last few years has been worse than hoped for.

Both point and non-point sources, like stormwater, have always been important to address. It is helpful to understand how stormwater and other non-point sources of pollution impact the estuary. So, it’s less about one versus the other because they’re both important. How they impact the Bay in different ways will be helpful to understand better. This will be a great question to talk about more in our Technical Advisory Committee meeting later this summer.

Over the past several decades, partners have made significant progress reducing nitrogen from point sources (such as wastewater treatment plants). But they are a smaller part of the challenge. Most of nitrogen entering the estuary comes from non-point sources, like stormwater runoff. These non-point source challenges have been relatively more important to understand and manage.

For example, stormwater carries nitrogen, sediment (which is pollution), and other organic materials into the estuary. More intense and frequent rain events deliver all these stressors to the entire Great Bay Estuary. Because it is an enclosed area of the estuary with less circulation, these factors impact is Great Bay proper especially. Furthermore, three different tributaries (rivers) discharge directly into Great Bay proper. Of these three, the Lamprey River has the greatest discharge.

Finally, the fine sediments in Great Bay are most susceptible to re-suspension and holding on to past pollution. It’s like trying to mop up a muddy floor while people keep tracking in more dirt. You can clean, but if new mud keeps coming in, it’s hard to see the progress.

There is not one single problem. There are many stressors. Our monitoring shows that the amount of CDOM in our waters is increasing, but our current scientific understanding in the Great Bay Estuary leads scientists to focus more on nutrients and sediments, not CDOM.

Why are nutrients and sediments more of a stressor than CDOM? CDOM actually only blocks some of the light that eelgrass uses for photosynthesis, but not all of it. In contrast, high nutrient levels lead to more production of plankton, seaweed and other organic matter, which can block all the light that eelgrass needs for energy.

For a more in-depth look on the relationship between CDOM, light, and eelgrass, please see our recent report: Development of a Great Bay Bio-Optical Model.

No, but it does makes eelgrass recovery more challenging.

Increased rain is harder on eelgrass. It leads to more stormwater runoff which both stirs up Great Bay proper and increases pollution deposited to the estuary. When PREP and partners completed the Eelgrass Resilience Project (published in 2024), we gained a much deeper understanding of how vulnerable eelgrass is to these rainfall-driven changes.

During 2021 and 2023, we had unusually heavy precipitation during the eelgrass growing season (which typically takes place April through August). These growing seasons ranked among the four wettest in a twenty-year period (2003-2023) on record. For context, the wettest growing season in the past 20 years was the 2006 Mother’s Day Flood (32.15 inches of rain). However, having extreme rainfall back-to-back had a significant, negative impact on eelgrass. In some ways, we are lucky to be able to study and understand that significance. The Eelgrass Resilience Project ultimately documented a system under stress, rather than a recovering ecosystem as we had originally envisioned.

Warmer air and water also makes things harder for eelgrass, because that warmer water speeds up eelgrass’ metabolism. When this happens, eelgrass has a need to “eat more food” to keep up with its metabolic needs. “Eating more food” for eelgrass means grabbing more photons for photosynthesis: more light. In order to support eelgrass, we need to support our ecosytem in having clearer water than it used to. This is challenging but it’s do-able.

Over time, we have seen seaweed and phytoplankton increase. Since 2022, however, Great Bay proper has been so stirred up that even seaweed and phytoplankton abundance has decreased.

Our 2023 State of our Estuaries Report showed that phytoplankton levels have increased at two sites in Great Bay, but it has decreased at other sites. Seaweeds have certainly increased since the 1970s. We saw a lot of seaweed in the Bay between 2010 and 2022. Seaweeds and plankton need light just like eelgrass but they need much less than eelgrass.

At the same time, seaweed needs more nitrogen. This is why, around 10 years ago, there was concern that our system was becoming more favorable to seaweeds and plankton and less favorable for eelgrass. Eelgrass needs low nitrogen and very clear water.

Since 2022, however, the water in Great Bay proper has been so cloudy (turbid) that even seaweed and plankton have struggled. Again, this is why we need to reduce pollution, control stormwater and conserve land.

The science suggests that we can have fish, eelgrass and oysters in the future, if we continue to improve water quality and implement restoration. The rationale for monitoring is to make sure that we continue to decrease the stressors we have control over. Then, we continue to check to see how the environment responds.

Similar to improving the health of a human being, we combine case studies from other people with detailed measurements of what’s going on in our particular system. Without these detailed measurements, it becomes very difficult to understand what we’re seeing and why.

We also use monitoring to better understand how to improve our restoration efforts.

Therefore, we continue to monitor the pollution we put into our system, how it affects water quality (such as nutrients levels, sediments, and water clarity), and ultimately, how those changes impact the things we care about, like salt marshes, fish, eelgrass, and shellfish.

Stay with the plan of reducing pollution and conserving land where we can with more urgency.

Working for a community involves a lot triage and managing priorities. Municipalities have been doing great work to reduce pollution and keeping an eye on the eelgrass health. We’ve all hoped the eelgrass would start to respond to the progress we’ve made, but that’s not the case. It’s time adjust priorities.

Ecoystems are dynamic and you can’t “set it and forget it.” Rather, you try a few science informed options and see what happens. Then you react. For example, if we have regular rainy springs, we may require more urgent pollution reduction and stormwater management.

If we want to continue to have a watershed that is economically strong and a beautiful, healthy place to live, water quality needs to be a higher priority.

Oysters and eelgrass share stressors but they also have distinct stressors. One thing they both share: turbid (cloudy) water is big challenge for both species.

Back in the 90’s, we had over 20 million oysters in the Estuary and over 2,500 acres of eelgrass in the Estuary. Now, we have around 5 million oysters and just over 200 acres in the Great Bay Estuary.

The loss of eelgrass hurts oysters and vice versa. Both of these habitats reduce nutrients and calm the water down so sediments can settle to the bottom. With such large decreases in both habitats, it becomes a bit of a vicious circle. This means it’s more important than ever to reduce pollution, conserve land and restore these habitats.

Eelgrass is a fantastic nursery habitat for juvenile fish and crustaceans. Losing eelgrass is certainly hard on the fish that spend part of their lives in the Estuary, such as herring and flounder.

In the 90s, a juvenile herring making its way out to the ocean for the first time, or returning back to freshwater to spawn, could pick it’s way through the entire estuary and use eelgrass and oyster reefs for cover most of its way. That is no longer possible due to the loss of these habitats. It is a well-known fact that 50% of the fish we consume depend on estuaries at some point in their lives.

This only underscores how important it is for us to reduce pollution, develop more sustainably, conserve more land, and put more energy into restoration.