Environmental Protections Under Siege as Illinois Agencies Clash Over Endangered Species and Infrastructure Demands
In the winding creeks and sediment-rich rivers of southern Illinois, the presence of the bigeye shiner—a delicate, translucent freshwater fish roughly the size of a paper clip—is considered a primary indicator of high water quality. Listed as an endangered species in Illinois, the shiner has managed a tenuous survival despite a century of habitat degradation caused by industrial agricultural runoff and aggressive land development. Today, however, the greatest threat to this indicator species may not be the runoff itself, but a burgeoning bureaucratic civil war between the state’s primary environmental regulator and its largest public landowner.
Internal documents obtained through public records requests by WBEZ Chicago and Grist reveal a deepening rift between the Illinois Department of Natural Resources (IDNR) and the Illinois Department of Transportation (IDOT). At the heart of the dispute is a fundamental disagreement over how, and even if, the state’s Endangered Species Protection Act should be enforced when it conflicts with the timeline and budget of road and bridge construction. The standoff has reached a tipping point, with IDNR recently revoking a decade-old agreement that allowed IDOT to fast-track environmental reviews, citing a pattern of the transportation agency ignoring scientific recommendations.
The Union County Standoff and the Rationale of Escape
The friction became public last summer during a routine mapping project in Union County. IDNR regulators, acting on their mandate to protect the state’s 513 listed species, recommended that IDOT crews conduct a formal survey to determine if the bigeye shiner was present at a proposed construction site. If the fish were found, IDNR requested that IDOT apply for an Incidental Take Authorization (ITA)—a specialized permit that allows for the accidental harm or killing of a protected species provided that the developer takes specific steps to minimize the impact.
IDOT’s response was a blunt rejection of the expertise of state biologists. In correspondence that has since become a focal point of the controversy, IDOT officials argued that such surveys were unnecessary because "fish swim away." This simplified view of aquatic biology—that mobile animals will naturally vacate a construction zone to avoid noise and physical disturbance—is one that IDNR scientists have vehemently contested.
"We are the experts," Todd Strole, IDNR’s assistant director, wrote in an internal email earlier this year. "Fish are not the same; some don’t swim away."
The biological reality is far more complex than IDOT’s "swim away" theory suggests. Many of the species in question, such as the American brook lamprey, spend significant portions of their life cycles burrowed deep within the riverbed sediment. Others, like various species of state-endangered mussels, are sessile and cannot move at all. For these creatures, the arrival of heavy machinery or the discharge of silt and debris is a death sentence, regardless of the noise levels.
A History of State-Level Protections and the ITA Process
To understand the weight of this dispute, one must look at the legal framework governing Illinois’ wilderness. The Illinois Endangered Species Protection Act was signed into law in 1972, predating the federal Endangered Species Act (ESA) by a year. It established the Illinois Endangered Species Protection Board and gave the IDNR the authority to list species and regulate activities that might harm them.
The primary tool for this regulation is the Incidental Take Authorization. The ITA process is rigorous by design. It requires an applicant to:
- Conduct thorough biological surveys to determine species presence.
- Submit a conservation plan outlining how they will minimize the "take" (harm or killing).
- Demonstrate that they have the funding to implement these mitigation measures.
- Engage in a public comment period to allow citizens and environmental groups to weigh in.
This process typically takes five to six months. For IDOT, which manages thousands of miles of roads and hundreds of bridges, these months are viewed as a costly delay. In one instance in White County, IDOT officials claimed that relocating endangered mussels would delay a project by an entire construction season and add approximately $2 million to the taxpayer-funded budget.
However, IDNR officials argue that these costs are the price of legal compliance. Without an ITA, any unintentional killing of a state-listed species can technically result in criminal charges. By bypassing the permit process, IDOT may be exposing the state to legal liabilities while simultaneously undermining the spirit of the law it is bound to uphold.
Chronology of a Breakdown: From Cooperation to Cancellation
The relationship between the two agencies has been deteriorating for several years, but the timeline of the current crisis began in early 2019 when a long-standing memorandum of understanding between the two departments expired. This agreement had previously allowed IDOT to streamline its environmental reviews, operating under a degree of autonomy that assumed the agency would follow IDNR’s baseline recommendations.
Despite the expiration of the agreement, IDOT continued to conduct its own environmental reviews for nearly four years. During this period, IDNR officials observed what they described as an "apparent automatic response" by IDOT to decline recommendations for ITAs. According to public records, IDOT may have overridden the Endangered Species Protection Act in at least 11 separate cases over the past year alone.
The tension culminated in the fall of 2023, when Bradley Hayes, IDNR’s impact assessment manager, sent a formal cancellation letter to IDOT. The letter officially terminated the agency’s ability to fast-track its projects, forcing every transportation project back into the standard—and slower—review pipeline.
"Planning and engineering needs don’t negate or override the recommendations by scientists," wrote Ann Holtrop, head of IDNR’s division of natural heritage, in an email reflecting the agency’s frustration.
The National Context: A Growing Trend of Rollbacks
The dispute in Illinois does not exist in a vacuum. It mirrors a broader national trend where environmental protections are being weighed against infrastructure and industrial expansion. The federal Endangered Species Act, which has been credited with the recovery of iconic species like the bald eagle and the grizzly bear, has faced consistent pressure from various administrations.
During the Trump administration, significant moves were made to weaken the ESA. This included the convening of the "God Squad"—a high-level committee with the power to exempt projects from the ESA entirely—to facilitate oil drilling in the Gulf of Mexico. More recently, the administration proposed a rule to redefine the term "harm" within the law, a move that critics say would make it significantly harder to prosecute companies for habitat destruction.
While the Biden administration attempted to reinstate many of these protections, the pendulum has continued to swing. In Illinois, the silence of Governor JB Pritzker’s office on the matter has raised questions. When asked for comment on the internal rift, the Governor’s office deferred to a joint statement from IDOT and IDNR, which claimed the agencies are currently drafting a new, "updated" agreement.
The joint statement, issued by IDOT spokeswoman Maria Castaneda, emphasized that IDOT considers "multiple factors, including known information about the species, other environmental surveys, engineering, costs, and public safety." This phrasing, however, suggests that biological expertise is merely one variable in a larger equation, rather than a legal mandate.
Implications for Biodiversity and Public Accountability
The implications of this inter-agency clash extend far beyond the fate of a single fish in Union County. If the state’s largest landowner and developer is permitted to selectively follow environmental laws, it sets a precedent that could be adopted by private developers and other public entities.
Ecologically, the "fish swim away" philosophy ignores the reality of habitat fragmentation. Even if a fish does swim away from a construction site, it is often forced into territory already occupied by other populations, leading to increased competition for food and breeding grounds. For species like the harlequin darter or the American brook lamprey, which have very specific habitat requirements, there may be nowhere else to go.
Furthermore, the lack of transparency in how these decisions are made—revealed only through leaked internal emails and FOIA requests—points to a crisis of accountability. The ITA process includes a public comment period for a reason: to ensure that the public’s interest in preserving biodiversity is balanced against the need for infrastructure. By bypassing this process, IDOT effectively removes the public from the conversation.
Conclusion: Seeking a New Path Forward
As IDOT and IDNR work to draft a new agreement, the scientific community remains wary. The core of the conflict remains unresolved: Should engineering and budgetary constraints have the power to override the biological assessments of the state’s designated experts?
The bigeye shiner, the harlequin darter, and the American brook lamprey serve as the "canaries in the coal mine" for Illinois’ waterways. Their decline is a signal of a degrading ecosystem that eventually impacts human health and water security. Experts argue that the cost of protecting these species—while sometimes high in the short term—is negligible compared to the long-term cost of losing biodiversity and the legal integrity of the state’s environmental framework.
For now, the standoff continues. Construction projects move forward, permits remain unfiled, and in the quiet creeks of southern Illinois, the shiners continue to dart through the water—unaware that their survival depends less on their ability to swim away and more on the outcome of a bureaucratic debate in Springfield.
