In what it calls a case of “exceptional importance,” the Florida Department of Environmental Protection (FDEP) is now asking a federal appeals court to overturn major rulings that require it to take specific steps to protect manatees in the northern Indian River Lagoon — a critical habitat where hundreds of manatees have died in recent years.

This week, the FDEP filed a 56-page brief with the 11th U.S. Circuit Court of Appeals, aiming to challenge U.S. District Judge Carlos Mendoza’s orders that found the agency in violation of the Endangered Species Act. Mendoza’s ruling included a moratorium on new septic tanks in Brevard County and nearby areas, and mandated programs to help manatees recover, such as biomedical assessments and supplemental feeding during periods of starvation.

The FDEP isn’t just disputing the order — it’s challenging its very role. The agency argues that wildlife protection responsibilities fall under the Florida Fish and Wildlife Conservation Commission, not DEP. It claims the court overstepped by asking the “wrong agency” to enforce federal environmental protections.

But let’s not lose sight of what triggered this legal battle.

In 2021, Florida recorded a devastating 1,100 manatee deaths — many linked to the collapse of seagrass beds in the Indian River Lagoon. Without this essential food source, manatees starved. The collapse has been largely tied to nutrient pollution from wastewater and septic runoff, which fuels harmful algae blooms that choke out seagrass.

In response, the environmental group Bear Warriors United filed a lawsuit in 2022. They alleged that FDEP’s septic permitting practices contributed to the continued decline of water quality — and ultimately, to the manatee die-off. They demanded accountability.

Judge Mendoza agreed. In his rulings this spring, he stated that the lagoon’s condition would likely take a decade or more to recover, even with corrective action. His order directed the state to seek an “incidental take” permit from the U.S. Fish and Wildlife Service — a formal acknowledgment that state-permitted activities are likely harming a federally protected species.

But DEP’s latest filing argues the science — and the responsibility — aren’t so clear. Their attorneys say Bear Warriors United lacks legal standing, claiming the connection between DEP permits and manatee deaths is too speculative. They also point to storm damage, hurricanes, and legacy sewage infrastructure as contributing factors — not just septic tanks.

According to their brief, the agency has taken enforcement actions against municipalities for untreated sewage discharges and argues that these broader issues are being unfairly pinned solely on the DEP.

Still, the numbers paint a troubling picture. After the peak of 1,100 deaths in 2021, manatee deaths dropped slightly to 800 in 2022, then 555 in 2023, and 565 so far in 2024. But as of mid-July, 477 deaths had already been reported this year — with Brevard County leading the state again.

Manatees remain listed as a threatened species under federal law, and their survival is intrinsically linked to the health of Florida’s waterways. The Indian River Lagoon, once teeming with seagrass meadows and marine life, is now one of the clearest indicators of how quickly a system can collapse under environmental stress — and how long it can take to recover.

Whether the appeals court sides with the DEP or upholds the lower court’s decision, this case is a wake-up call. Bureaucratic boundaries aside, Florida’s ecosystems — and the species that depend on them — can’t afford decades of inaction.