Unassessed Waters
Beyond Our Namesake
From the origin of its headwaters in upstate New York and its southern journey through a succession of water gaps on a zigzag path through 284 miles of Pennsylvania’s rural heartland to its final destination at the northern end of the Chesapeake Bay in northeastern Maryland, the Susquehanna River has long been the defining feature of our region.
The Susquehanna shapes communities, sustains ecosystems and connects us to one of the largest watersheds in the world. Yet, like so many of the nation’s major waterways, it faces ongoing environmental challenges. From sediment buildup to nutrient pollution and habitat degradation, they all threaten the health of the river and the Chesapeake Bay it feeds into.
At Susquehanna University’s Freshwater Research Institute, a dedicated team of researchers, students and conservation partners don’t just study the problem. They’re leading the charge in watershed restoration, actively improving the health of our river and safeguarding its vitality — and that of the Chesapeake Bay’s — for generations to come.
Where Science Meets Action
Recognizing the urgency of these challenges and with the assistance of a grant from the Richard King Mellon Foundation, Susquehanna University launched the FRI in 2014 as a hub for science-based conservation and hands-on student training. Working in close partnership with local landowners, government agencies and conservation organizations, the Institute is pioneering watershed restoration projects that address the root causes of pollution.
With a drainage basin spanning more than 27,500 square miles, including nearly half the land area of Pennsylvania, the Susquehanna River is the largest tributary to the Chesapeake Bay and provides half of its freshwater. But centuries of agricultural runoff, deforestation and industrial pollution have taken a toll on the river’s overall health. Excess nutrients frequently choke the water with algae blooms, sediment clouds the riverbed and native fish populations — once abundant — struggle to survive in a rapidly changing environment. What happens in central Pennsylvania doesn’t just stay here; it ripples downstream, affecting ecosystems, economies and communities throughout the region.
“We all have a stake in the health of our waterways.”
Matt Wilson, Director of the FRI and CEER Field Station
“Though the problems and solutions are complex, our mission is very simple: to protect and restore freshwater ecosystems through hands-on research, education and community collaboration,” says Matt Wilson, director of the FRI and CEER Field Station. “We’re committed to making a measurable difference in the health of the Susquehanna River and beyond.”
Restoring Streams
One of the Institute’s most ambitious efforts is its large-scale stream restoration work and riparian buffer planting.
Many of the region’s waterways have been straightened, channelized or stripped of their natural vegetation, leaving them vulnerable to erosion. FRI scientists, along with student researchers, are helping to reverse that damage by restoring streams to their natural meandering paths and original floodplains, stabilizing eroded banks and replanting native vegetation. These interventions reduce sediment pollution, improve water clarity and create critical habitats for fish, insects and birds.
Wilson sees firsthand how these restoration projects are reshaping the landscape.
“We’re not just fixing streams; we’re reviving ecosystems,” he explains. “By restoring the natural curves of a stream, planting riparian buffers and reconnecting floodplains, we’re allowing these waterways to function the way they were meant to. And that has an enormous impact, not only on our local biodiversity but on the health of the Susquehanna River and the entire Chesapeake Bay.”
In addition to restoring streams, the FRI is addressing one of the biggest sources of pollution in the Susquehanna River: agricultural runoff.
Excess nitrogen and phosphorus from farms can cause massive algae blooms that deplete oxygen and create “dead zones” in the Chesapeake Bay. To combat this, students at the Institute work directly with local farmers to implement best management practices — such as cover cropping, no-till farming and the creation of wetlands — to filter runoff before it reaches the river.
“Our approach is about collaboration,” says Wilson. “Farmers are stewards of the land, and many of them want to be part of the solution. We’re helping to provide the science and resources to make that happen.”
A Partnership for Precision Conservation
Restoring a watershed as vast and complex as the Chesapeake Bay’s requires not only boots-on-the-ground restoration but also cutting-edge data and collaboration between conservation leaders. Acknowledging this, Susquehanna’s Freshwater Research Institute has enjoyed nearly a decade of collaboration with the Chesapeake Conservancy — one of the preeminent organizations dedicated to protecting and restoring the resources of the watershed and celebrating the people and places that shape the region.
The Chesapeake Conservancy, based on the shores of the bay in Annapolis, Maryland, is dedicated to protecting and restoring the natural and cultural resources of the Chesapeake Bay watershed. Recognized as a leader in precision conservation, the Conservancy uses advanced technologies like high-resolution mapping, geospatial data analysis and artificial intelligence to target where conservation efforts will have the greatest overall impact. The Conservancy’s work bridges the gap between traditional environmental stewardship and modern innovation, helping its network of conservation partners across the region — like the Institute and its student researchers — make informed, strategic decisions to benefit both the people and wildlife that call the watershed home.
Since 2016, Susquehanna’s FRI and the Chesapeake Conservancy have worked together to implement these precision conservation strategies — specifically the Conservancy’s sophisticated mapping tools — to identify the most critical areas for restoration and the most effective land parcels to restore. By leveraging this technology, the FRI’s student researchers can maximize the impact of their conservation efforts, ensuring that every tree planted and every streambank restored contributes meaningfully to the greater health of the watershed.
But the Freshwater Research Institute doesn’t just implement the Conservancy’s technology and relish its data. The Institute’s research lab literally houses the Chesapeake Conservancy’s Pennsylvania program — including seven staff members who also call the Freshwater Research Institute home — and collaborates with FRI staff and Susquehanna students to implement and study stream restoration projects in central Pennsylvania.
Together, the FRI and Chesapeake Conservancy operate a network of water quality monitoring stations that provide real-time insights into nutrient levels, sediment loads and overall ecosystem health. This data helps researchers refine restoration strategies and advocate for science-based policy decisions.
This partnership was formalized in 2023 through a memorandum of understanding, which underscored a shared commitment to advancing ecological restoration in the region and beyond. The agreement strengthens ongoing collaborations, merging the Institute’s rigorous scientific research with the Chesapeake Conservancy’s expertise in landscape-scale restoration. Perhaps most significantly, the partnership serves as a model for how universities and conservation organizations can work together to tackle large-scale environmental challenges. By integrating academic research with real-world conservation, Susquehanna’s Freshwater Research Institute and the Chesapeake Conservancy are demonstrating that science and action can, and must, go hand in hand.
“We all have a stake in the health of our waterways,” says Wilson. “What happens in Pennsylvania affects the Chesapeake Bay, and what we do today shapes the future of our environment. By working together, we can create lasting change.”
Equipping the Next Generation of Conservation Leaders
A defining aspect of the Freshwater Research Institute’s work is its commitment to student involvement. Susquehanna University students don’t just study watershed science in the classroom — they immerse themselves in the work from their earliest days on campus, conducting field research, collaborating with conservation partners, analyzing data and even presenting their findings to policymakers.
Student research plays a vital role in collecting data that guides overarching restoration strategies. They help monitor water quality at dozens of sites, measuring everything from nutrient levels to macroinvertebrate populations, which serve as indicators of stream health. Their work contributes to regional and national efforts to track the health of the Susquehanna River and, ultimately, the Chesapeake Bay watershed.
“I spend time each summer at the Institute as one of its ‘stream team’ interns, helping to conduct stream surveys and supporting other collaborative restoration and research initiatives between the FRI and its strategic conservation partners,” says Paige Hepfer ’26, an ecology and advertising & public relations double major from Tioga, Pa.
Through her internship with the Institute, Hepfer works closely with the Northcentral Pennsylvania Conservancy, the Middle Susquehanna Riverkeeper, the Pennsylvania Fish and Boat Commission, and various county conservation districts to help with conservation efforts, community outreach and education, research and data collection.
“The Institute has given me so much confidence to conduct research in both field and lab settings and, because of its embrace of experiential learning, I’m able to apply the concepts I have learned in class to real, meaningful work,” she says. Read more about Paige’s experiences at the FRI in the End Notes column she penned for this issue.
Beyond research opportunities, the Freshwater Research Institute — again in partnership with the Chesapeake Conservancy — launched a workforce development program to prepare Susquehanna students for careers in conservation.
Since the summer of 2023, student researchers have been trained and certified as herbicide applicators to manage invasive plant species within watershed restoration sites. They’ve also worked closely with regional partner organizations to learn about their programs, install restoration structures and plant trees, and attend weekly professional development workshops hosted by Susquehanna.
“We teach our undergraduate students the skills they will need as habitat restoration specialists while they simultaneously conduct much-needed maintenance work on 50 acres of existing restoration sites, where our partner organizations are in real need of help,” Wilson says. “Most of the places where we add fencing and plant trees are on farms where invasive species are common. We need to do something to keep that growth at bay until the newly planted trees are mature.
“Our students are doing that very real, very necessary work,” he adds.
Anyone who applies or supervises the application of certain pesticides must be certified in accordance with Environmental Protection Agency regulations and state laws. Certification involves a written exam, and, for the Institute’s students, it also includes a week of hands-on experience and several check-ins throughout the summer with their course instructor.
“As conservation efforts grow in the Chesapeake Bay watershed, workforce capacity is an emerging barrier to achieving tree canopy, riparian forest buffer and climate resilience goals outlined in the Chesapeake Bay Watershed Implementation Plan,” says Adrienne Hobbins, the Chesapeake Conservancy’s Pennsylvania program manager. “Many local and state governments, environmental consulting firms and nonprofits throughout the watershed have had difficulty filling entry-level positions to keep up with the pace of conservation funding and accelerating landowner willingness. The certification that this program awards is one that is in high demand for restoration work.”
In addition to their herbicide certification, student researchers learn about assessment and monitoring methods for stream health. One of the first workforce development trainings offered by the Institute and Conservancy focused on habitat assessment, which provides crucial data that the Department of Environmental Protection uses to add or remove a stream from its list of impaired waterways.
“We have been fortunate to partner with Susquehanna University and the Chesapeake Conservancy on many restoration projects and stream monitoring sites,” says Savannah Rhoads ’18, an ecology alumna and watershed specialist with the Union County Conservation District.
“The major hurdle we face is a lack of technical assistance — there simply aren’t enough agencies with the required skills to design and implement the work,” she adds. “Programs like this one, which are developed to train and certify future employees, are integral to our ability to maintain, complete and take on new conservation projects moving forward.”
“As we act to address a changing climate and restore forests, cultivating the next generation of stewards is a big part of the solution,” said Pennsylvania Department of Conservation and Natural Resources Secretary Cindy Adams Dunn. “We need all the help we can get, so the department applauds and supports this effort to engage young people in conservation work.”
Wilson emphasizes that getting students involved in real-world conservation isn’t just about education — it’s about building the next generation of researchers, policymakers and advocates who will carry this work forward.
“Future scientists need hands-on learning opportunities like those I enjoyed at Susquehanna,” says Danielle Tryon ’24.
As an ecology and earth & environmental sciences major, Tryon worked with the FRI as a stream team summer intern and coordinator of its Environmental Education & Outreach Program.
“When I first started college, it was my goal to take advantage of every opportunity Susquehanna had to offer,” she adds. “Through my experiences at the FRI, I gained knowledge, field experience and a deeper commitment to preserving our natural world — especially our aquatic ecosystems.”
Today, Tryon is pursuing a Master of Science in fisheries at the University of Alaska Fairbanks. Specifically, she studies Chinook salmon migration and habitat use along the Kenai River.
“This opportunity marks an exciting new chapter in my career, and I couldn’t be more grateful for the support, guidance and encouragement I received from my mentors and peers at the Freshwater Research Institute,” Tryon says. “I can’t wait to grow as a scientist and contribute to fisheries research.”
Expanding Collaboration
“The Chesapeake Conservancy may be our largest partner,” Wilson says, “but by no means have they been our only partner in recent years.”
In parallel, and occasionally in tandem, the Freshwater Research Institute has leveraged private foundation funds to place student researchers in partner organization internships for environmental education, recreation, advocacy and conservation. Occasionally, these internships are even supported by alumni like Rhoads.
“Future scientists need hands-on learning opportunities like those I had at Susquehanna.”
Danielle Tryon ’24
“I’m so proud to collaborate with my alma mater,” Rhoads says. “Doing so has enabled me to connect with students, offering them real-world experience and insight into the operations of a conservation district while actually completing more stream restoration projects.”
Students interning with Rhoads and the Union County Conservation District have worked with farmers and other landowners; and have installed in-stream restoration structures alongside Fish and Boat Commission staff. Others interning with the Susquehanna Greenway Partnership have led outreach programs across the region and worked on trail designs, and Middle Susquehanna Riverkeeper Association interns have taught environmental education programs on an 80-foot paddlewheel riverboat and sampled streams across the watershed for pollution. To acquire these placements, FRI students complete common internship application forms and are matched with partner organizations based on mutual interests.
Tryon, who, in addition to pursuing fisheries studies also works as a lead technician for the Alaska Department of Fish and Game, credits her internship with the Riverkeeper Association for helping her develop community relations skills — which are vital for conservation professionals.
“My internship with the Riverkeeper Association gave me so much insight,” she says. “I am so thankful for the opportunities I had as an undergraduate to communicate with residents of the watershed and to educate them about the ways in which they too can protect and promote the Susquehanna River, its tributaries and the aquatic ecosystem it supports.”
Like Tryon’s experience, the internships completed by Freshwater Research Institute students translate into real-world — and often very local — outcomes. For example, one in seven watershed specialists for conservation districts located within the Susquehanna River watershed are recent Susquehanna University graduates who worked with the Institute or its network of conservation partners. Others have gone on to work for restoration consulting firms, state and federal agencies, watershed organizations and environmental education centers.
The Ripple Effect
The success of Susquehanna’s Freshwater Research Institute’s is not measured just in cleaner water and thriving fish populations, but in the ripple effect they create. Every acre of restored floodplain, every mile of replanted streambank and every farm that reduces its nutrient runoff contributes to a healthier Susquehanna River. The impact extends beyond Pennsylvania’s borders, influencing everything from blue crab populations in Maryland to the water quality of coastal communities.
“There’s no single solution to protecting our freshwater resources,” says Wilson. “But every effort — big or small — adds up. We’re proud to be part of the solution and to inspire the next generation of environmental leaders.”
Despite these successes, the work is far from over. Climate change is intensifying the challenges facing the Susquehanna River, bringing more extreme weather patterns and increasing the urgency of restoration efforts. The Freshwater Research Institute is actively researching how best to build resilience into the ecosystem, ensuring that the progress made today can withstand the challenges of tomorrow.
“Rivers are living systems,” Wilson says. “If we take care of them, they’ll take care of us. That’s what drives our work — it’s not just about fixing what’s broken but ensuring that these waterways remain vibrant and resilient long into the future.”
Beginning with Native Brook Trout
Less than 10% of Pennsylvania’s streams have been systematically surveyed for the presence of native brook trout, which leaves the other 90% vulnerable. When brook trout are identified in a stream, their protection becomes a priority, which, in turn, influences the designated water and land usage in the area surrounding the stream.
Since 2010, Susquehanna student researchers have surveyed approximately more than 850 of the 6,000 stream segments in the Pennsylvania Fish and Boat Commission’s Unassessed Waters Initiative, a program to survey and monitor unassessed streams throughout Pennsylvania to identify and protect wild trout populations, with the goal of updating the commission’s list of wild trout waters.
There are more than 86,000 miles of streams and rivers in Pennsylvania, more than in any state in the continental U.S. Prior to the Unassessed Waters Initiative, the PFBC had no data on the small streams and creeks that Susquehanna’s Freshwater Research Institute has been surveying. Susquehanna’s field work has contributed to more than 200 streams being added to the PFBC’s Wild Trout Waters list — giving these waterways permanent protection.
“The Freshwater Research Institute’s partnership with the Unassessed Waters Initiative provides Susquehanna students with an invaluable opportunity to influence conservation policy through hands-on scientific research,” says Kathy Straub, dean of Susquehanna University’s School of Natural & Social Sciences and professor of earth & environmental sciences.
“It’s a powerful example of how science drives real-world change,” she adds.
