TALLAHASSEE, Fla. – A federal judge Monday ordered the Florida Department of Environmental Protection to take a series of steps aimed at protecting manatees in the northern Indian River Lagoon, including requiring it to go through a federal permitting process and temporarily preventing new septic tanks in the area.

U.S. District Judge Carlos Mendoza also ordered establishment of programs to conduct biomedical-health assessments and supplemental feeding for manatees.

Mendoza’s order came after he ruled April 11 that the state violated the Endangered Species Act in the northern Indian River Lagoon, which is primarily in Brevard County but also goes into southern Volusia County. Mendoza sided with the environmental group Bear Warriors United, which argued that wastewater discharges into the lagoon led to the demise of seagrass, a key food source for manatees, and resulted in deaths and other harm to manatees.

While the state has appealed the April 11 ruling to the 11th U.S. Circuit Court of Appeals, Mendoza on Monday issued a permanent injunction designed to carry out his decision.

A key part of the order is for the state to seek what is known as an “incidental take” permit from the U.S. Fish and Wildlife Service. That process would include the state developing a conservation plan, which could provide “permanent protection and management of habitat for the species,” according to information about such permits on the federal agency’s website.

While the incidental-take permit request is pending, Mendoza ordered the Department of Environmental Protection to not issue permits for constructing and installing septic systems in a northern Indian River Lagoon watershed. That moratorium will start July 17 and continue until the incidental-take permit is issued, according to the order.

Septic tanks discharge nitrogen, which can cause harmful algae blooms. Bear Warriors United asked Mendoza to halt construction of new septic systems until an incidental-take permit was in place.

“New residential and commercial construction that use (septic tanks) will only exacerbate nitrogen loading into the North IRL (Indian River Lagoon),” the group’s attorneys wrote in an April 25 court document. “The court has already held that continuing high levels of nitrogen loading into the North IRL has caused the collapse of seagrasses, resulting in ongoing take of manatees that occupy the North IRL.”

But in a May 6 response, Department of Environmental Protection attorneys said such a moratorium would “improperly bind parties” that are not in the case.

The department’s attorneys wrote that Bear Warriors United was seeking an “injunction that, on its face, prohibits anyone from undertaking residential or commercial construction using onsite sewage treatment and disposal systems. Needless to say, the independent landowners and builders whose property rights would be curtailed by such an order are not parties to this action.”

Until the state receives an incidental-take permit, Mendoza also ordered the establishment of biomedical-assessment and supplemental-feeding programs for manatees in the area. He directed that the programs be overseen by “manatee experts” and that quarterly reports about the programs be made public.

Bear Warriors United filed the lawsuit in 2022, after Florida had a record 1,100 manatee deaths in 2021, with the largest number, 358, in Brevard County. Many deaths were linked to starvation.

The state had 800 manatee deaths in 2022, before the number dropped to 555 in 2023 and 565 in 2024, according to Florida Fish and Wildlife Conservation Commission data. As of May 9, 363 manatees deaths had been reported this year, including 75 in Brevard County.

Manatees are classified by the federal government as a threatened species.