In the hot, dry expanse of the Chihuahuan Desert, the Pecos River winds through southeastern New Mexico and western Texas. Its deep pools and slow-moving channels are lifelines for wildlife in one of North America’s harshest landscapes. Yet for the Rio Grande cooter, a freshwater turtle listed as threatened in New Mexico and a species of concern in Texas, survival is far from certain.

Human activity and environmental changes have reshaped its habitat across the Rio Grande Basin — from the Pecos River to the Texas-Mexico border — shrinking areas where turtles can feed, rest and reproduce. In some 300-kilometer stretches of the Pecos, conditions are so poor that turtles are nearly absent. Even resilient adults face stress from rising salinity while juveniles struggle to survive.

Despite these challenges, small but meaningful refuges remain. Tributaries like Independence Creek in Texas and the Black River in New Mexico offer cleaner water, stable flow and reduced human disturbance, giving the species a chance to survive.

Conservationists and researchers actively monitor these waterways to assess population health, habitat conditions and environmental stressors affecting the Rio Grande cooter. Among them is Ivana Mali, the Ecology Wildlife Foundation Distinguished Professor for Conservation Biology at North Carolina State University’s College of Natural Resources.

Over the past decade, Mali has conducted intensive field studies in the Pecos River and its two tributaries, the Black and Delaware rivers, using techniques such as trapping, mark–recapture and habitat surveys to study population dynamics, growth, survival, movement, reproductive success and responses to environmental factors like drought and river flow.

Secrets of a Hidden Species

During her graduate studies at Texas State University, one of Mali’s advisors told her, “We’re going to lose the Rio Grande cooter; it’s not a question of if, but when.” The remark caught her off guard but crystallized the urgency of the situation, fueling her determination to study and conserve the little-studied species.

At the time, researchers recognized the Rio Grande cooter faced environmental pressures, yet little was known about its ecology and natural history. Its secretive habits, low population density and remote river habitats made it especially difficult to observe in the wild.

Mali’s early research established the Rio Grande cooter’s diet, reproduction and nesting behavior. Over time, she expanded into long-term field research and demographic analyses, contributing more than a dozen publications that advanced scientific understanding of the species’ distribution and population health.

From 2016 to 2022, Mali and her students surveyed the Black River. Each spring and summer, they trapped turtles, marked them with unique identifiers and released them, building a robust capture–mark–recapture dataset. With the assistance of Adam Duarte, quantitative ecologist and research wildlife biologist with the U.S. Forest Service, they developed several models showcasing population long term trends.

Their research found turtles in the Black River were relatively abundant and had high survival rates, with some variation between years. The river had a particularly large number of juvenile turtles, a sign of long-term persistence. However, surveys along the Pecos River, especially downstream of Red Bluff Reservoir, found very few turtles.

“After years of fieldwork, it’s evident that juvenile turtles persist in certain waterways like the Black River, but without steady recruitment and dependable river flows, populations remain fragile,” Mali said. “Understanding these patterns is essential not just for conserving this species but for guiding how we manage freshwater ecosystems under increasing stress.”

A Fragile River World

Unlike most freshwater rivers, the Pecos and other Rio Grande Basin tributaries naturally contain low to moderate levels of dissolved salts from surrounding geology and groundwater. Seasonal floods historically diluted these salts, maintaining freshwater conditions that allowed species such as the Rio Grande cooter to thrive.

Today, human activity and climate change disrupt these natural dynamics. Dams and reservoirs block seasonal floods that once refreshed habitats and maintained natural flows. Prolonged droughts reduce flow while oil extraction and fracking can release salts and pollutants into rivers and groundwater. Pools dry up, salinity rises and populations become isolated.

Rio Grande cooters are highly sensitive to changes in water flow, salinity and habitat conditions. They depend on deep, slow-moving pools that offer protection from predators, stable temperatures and plenty of aquatic plants for food and shelter during feeding, resting and mating.

Declining river flows and rising salinity shrink or even eliminate these pools, forcing turtles into harsher, saltier conditions. While Rio Grande cooters were likely adapted to the Pecos River’s natural salinity, reduced water flows now push them beyond their tolerance. Like other freshwater species, they lack specialized organs such as salt glands to remove excess salt from their bodies.

This can cause physiological stress, draining energy that would otherwise go toward growth and reproduction. “When salinity rises, it likely stresses their bodies and they may have to spend more energy searching for lower-salinity refuges instead of feeding, reproducing and performing other essential activities,” Mali said, which can reduce breeding success, weaken health and put isolated populations at greater risk of long-term decline.

Research supports these observations. In a 2022 study, Mali and collaborators found that Rio Grande cooters along the Pecos River were far less likely to occur in waters with salinity exceeding about 10,000 microsiemens per centimeter, a level comparable to industrial wastewater. In some areas, salinity is approaching that of seawater.

Elevated salinity can slow growth and increase stress in juvenile turtles, making them more vulnerable than adults, as demonstrated by a 2021 study on diamond‑backed terrapins. At the same time, adults can accumulate pollutants over their lifetimes and females may transfer some of these chemicals to their eggs, potentially affecting the next generation. 

Mali’s latest study, led by Ecology Wildlife Foundation Fellow Ana Sapp and published in the journal Environmental Toxicology, shows differences in contaminant levels in turtle blood and claws among the Pecos, Delaware and Black rivers, likely due to varying industrial pressures.

Tomorrow’s Turtles at Risk

The Rio Grande cooter is already under strain and conditions across the basin may grow more challenging. Climate stress and human activity are reshaping rivers near their ecological limits as drought reduces water availability and dams, withdrawals and development further alter flow and water quality.

Reservoirs such as Red Bluff Reservoir store and regulate flows for irrigation and municipal supply, while dams, diversion structures and groundwater pumping reduce the volume and timing of water downstream. These alterations disrupt natural flow patterns that historically sustained connected, functioning habitats.

Prolonged drought further stresses the Rio Grande Basin. The basin has faced extended drought in recent decades and climate projections suggest dry conditions are likely to continue or worsen. Rising temperatures, reduced snowpack and declining precipitation are expected to further limit river flows and water availability.

At the same time, oil and gas companies use vast amounts of freshwater for drilling and hydraulic fracturing, lowering river and stream flows. These operations generate large volumes of “produced water” — wastewater containing high concentrations of dissolved salts, hydrocarbons, heavy metals and other chemical compounds.

“We are likely witnessing ecosystem collapse in some stretches of the Pecos River.”

Much of this water is pumped deep underground, but injection does not eliminate risks. It adds pressure to the local water system and spills or leaks can still contaminate soil, groundwater and streams. In Texas, oil and gas companies have sought permission to release treated produced water into rivers such as the Pecos, while New Mexico regulators have blocked such discharges as lawmakers continue debating management strategies.

Field observations reveal how these changes are affecting the ecosystem. Mali noted that visible salt on plants along the Pecos River serves as a clear indicator of elevated salinity. “Even these subtle signs tell us the river system is under stress and changes in water chemistry like this can ripple through the ecosystem, affecting turtles and other freshwater species,” she said.

Looking ahead, drought, heavy water use and rising salinity threaten to push more stretches of the Rio Grande Basin beyond the limits freshwater species can tolerate. Changes in flow or water quality could reduce habitat connectivity, making it harder for populations to recover. Without action, these cumulative pressures could leave the Rio Grande Cooter increasingly vulnerable to long-term decline. 

Similar patterns have already been documented in fishes and macroinvertebrates, underscoring the severity of these changes. “Because turtles have a high tolerance for starvation and adults can persist in suboptimal environments, they are generally considered more tolerant than fishes and invertebrates,” Mali said. “Therefore, the fact that we are seeing similar effects in turtles is even more concerning; we are likely witnessing ecosystem collapse in some stretches of the Pecos River.”

Conservation in Action

For the Rio Grande cooter, survival depends on protecting key waterways such as the Black River and a few other tributaries and springs within the Rio Grande Basin. These habitats are among the few in the basin with stable conditions that support healthy adults and juveniles, making them vital strongholds. Elsewhere, turtles are sparse or isolated, emphasizing the need to protect these refuges and maintain river connections.

Rio Grande cooters lay their eggs on land but tend to stay close to the water’s edge, so even short gaps or dry stretches can cut populations off from each other, preventing turtles from moving between habitats. In degraded areas, adult turtles may survive for decades but few or no juveniles reach maturity, creating “ghost populations” that appear healthy but aren’t reproducing.

Maintaining connectivity within high-quality habitats allows Rio Grande cooters to move along rivers and streams — researchers have observed individuals traveling more than 30 kilometers within a single river system — to reach feeding and nesting areas. These movements help maintain genetic diversity, lower risks of isolation and inbreeding and support the species’ long-term resilience.

Scientists and conservation partners work to protect key habitats, maintain connections between rivers and tributaries and bolster Rio Grande cooter populations through monitoring, targeted habitat restoration, adaptive management strategies and collaboration with landowners, state agencies and local conservation organizations.

At ABQ BioPark in New Mexico, staff have raised Rio Grande cooters in captivity since 2017 as part of a broader conservation effort to develop care practices, refine head-starting techniques, strengthen genetic diversity and support struggling wild populations. The zoo has released some juveniles into the Black River.

Meanwhile, The Nature Conservancy has protected the 20,000-acre Independence Creek Preserve in West Texas since 1991. By working with local ranchers through easements and land purchases, the organization has helped keep the creek’s freshwater flowing and the surrounding watershed healthy. Its spring-fed waters also reduce salinity in the Pecos River below the creek’s confluence, creating ideal habitat for Rio Grande cooters, according to surveys.

While voluntary agreements with landowners provide important protections, conservation groups argue that stronger, enforceable regulations are necessary to ensure consistent safeguards for waterways in the Rio Grande Basin. They advocate measures to maintain minimum river flows, limit excessive water withdrawals and protect critical habitat, including federal protections by listing the Rio Grande cooter under the Endangered Species Act.

Scientists continue monitoring Rio Grande cooter populations, providing data to guide management, inform potential federal protections and support public awareness. Ongoing surveys and habitat assessments help researchers track population trends, identify emerging threats and evaluate whether additional conservation measures may be needed.

Funded by a grant from the New Mexico Department of Game and Fish, Mali and collaborators plan to resurvey Rio Grande cooter populations in the Black and Pecos rivers in summer 2026 to update their status. They will capture turtles to collect biological data, study habitat, assess threats and use statistical methods to estimate changes in population sizes while evaluating the health of individual turtles and how habitat conditions influence them.

“Long-term, sustained monitoring is our window into the lives of these turtles. By tracking their movements, population trends and other demographic data over years, we uncover patterns short-term studies would miss,” Mali said. “These insights show us what works, what doesn’t and where conservation efforts should be focused, providing the foundation for keeping rivers and the wildlife they support resilient.”