Simulating solutions: Auburn researcher uses computer modeling to address water quality and oyster survival in Alabama and beyond

Anna Linhoss grew up along the Chesapeake Bay, where locals could gather oysters the size of their shoes. Then came disease and pollution, wiping out the mollusks and transforming the bay’s ecosystem. 

That experience sparked an awareness of coastal issues and set Linhoss on a path to study oyster health, water quality and water flow.  

Today, as an associate professor in the Department of Biosystems Engineering in Auburn University’s College of Agriculture, Linhoss uses cutting-edge technology to tackle similar challenges alonhalong the Gulf Coast and beyond.

“I’m a modeler,” she said. “I build hydrodynamic models — virtual simulations of water flow and water quality — that help us understand how rivers, tides and storms interact with infrastructure and ecosystems.” 

From her modest desk in the Corley Building, Linhoss uses this work to predict flooding, guide restoration efforts and even help prevent mass die-offs of aquatic life.

Flooding in Mobile Bay

One project in Alabama has Linhoss and her students focused on the Causeway, a seven-mile land bridge connecting Mobile and Spanish Fort across the bay. The structure is prone to flooding during high tides or storms, disrupting traffic and introducing pollutants into the estuary, a unique zone where freshwater from the Mobile River mixes with saltwater from the Gulf Coast. 

“Estuaries are special places,” Linhoss said. “They’re breeding grounds for countless species, but when flooding adds pollutants, it threatens tourism, oyster production and the entire ecosystem.” 

Her models simulate water exchange and storm impacts, offering insights for redesigning the bridge and reducing flood risk. They also help identify optimal sites for oyster farms and restoration projects, which are critical for an industry facing new challenges. 

“Oysters aren’t just food,” Linhoss said. “They’re ecosystem engineers. They build reefs that protect shorelines, provide habitat and filter water.” 

For doctoral student Ali Maleki, who has degrees in civil engineering and water resource management from his native Iran, the work in coastal engineering is a natural fit. 

“This is a good opportunity for me to learn new software and advanced modeling,” he said. “Modeling is valuable for this project to show a relationship between water parameters such as changes in salinity and temperature.”

Along the coast

Disease and pollution that Linhoss witnessed as a teenager remain prevalent issues today, affecting water quality and ecosystems around the country. Her team is currently using models to pinpoint water conditions linked to outbreaks of a new disease called sudden unusual mortality syndrome that is killing oysters along the Mississippi and Alabama Gulf Coast. 

“Right now, we don’t know what is causing the disease,” she said. “Our work is to help figure out what water quality issues might be factors.” 

Alternatively, Linhoss knows what has caused oyster deaths in Louisianna, and it’s not a mysterious disease. 

The Bonnet Carré Spillway is a massive flood-control structure used to protect the nearby city of New Orleans. But diverting the mighty Mississippi River into Lake Pontchartrain and eventually the Gulf can come with a cost. 

Lake Pontchartrain is an estuary where fresh and saltwater mix. When the spillway was opened twice in 2019, Linhoss said the influx of freshwater dropped salinity levels near zero, triggering mass oyster deaths and stranding hundreds of dolphins and sea turtles along the Mississippi Sound, the coastal stretch between Louisiana and Alabama. 

“Our review shows that salinity is the most critical factor affecting oyster health, with temperature also playing a significant role,” Maleki said. “By modeling these conditions, we can identify patterns and develop solutions to address them.” 

Linhoss agreed, as experimenting with opening and closing the spillway is not feasible.  

“In the model, we can test different scenarios, like slower openings and different timing, and predict outcomes,” she said.

Beyond the classroom

By combining lessons from the past, like the Chesapeake Bay collapse, with tools for the future, Linhoss said, “We can propose management solutions and test them virtually. We can ask: What if we build a higher bridge? What if we restore oyster reefs here instead of there? What if we open the spillway differently?” 

Linhoss collaborates with colleagues across the country, as well as Auburn graduate students, who learn advanced computing and physics-based modeling, skills increasingly sought after in industry. They also see how science informs policy and practice. 

“Even if it’s just from a computer, what we’re learning will inform decisions that help farmers, engineers and construction projects,” Maleki said. “Our simulations can guide solutions for issues like flooding and oyster farm health.” 

For Linhoss, the stakes are clear: “Healthy waterways mean thriving ecosystems, resilient infrastructure and sustainable industries. Everybody loves going to the beach. Fishing is huge. But if water quality declines, fish disappear, wetlands erode and beaches become unsafe for swimming. It affects livelihoods and the places we love.  

“Whether you live on the coast or just love visiting, this work impacts you.”