Sea water encroaching on the Everglades will hamper decades of work by a government program to reverse manmade damage to the vast, fragile ecosystem at the tip of Florida, according to a new report published on Wednesday.

The federal, multibillion-dollar Comprehensive Everglades Restoration Plan, authorized by Congress in 2000, was designed to redirect fresh water, reducing sea water incursion in a long-term effort to bring the tropical wetland ecosystem back to the way it looked in the early 20th century, before influxes of people to southern Florida drained much of it for development. The region, known as the “river of grass”, is less than an hour’s drive from Miami but is home to mangrove forests and cypress swamps housing alligators, orchids, storks and ibises, as well as threatened species such as the Florida panther. But it has long struggled to recover from water diversions for agriculture, swelling communities and other forms of environmental degradation, such as fertilizer runoff.

Now a new report from the National Academies of Sciences, Engineering and Medicine warns that rising global temperatures are also changing the Everglades in ways the state and federal government must consider, including changing rainfall patterns and accelerating sea-level rise. “It is clear that the Greater Everglades of 2050 and beyond will be much different from what was envisioned at the time of the [plan],” the biennial report says.

The committee of independent scientists charged with advising the government says it’s time to re-evaluate the program, to consider what climate change will mean for the “interrelated challenges of restoring the natural system, providing flood protection, and meeting the water demands of a growing population”.

The committee chair, Bill Boggess, said current project plans did not adequately consider a range of possible sea levels. Sea levels were 3in above the 1993 average last year and will continue to go up, according to the US National Oceanic and Atmospheric Administration.

“Analyzing that what’s being built and being designed is robust to those conditions is really what we’re encouraging,” Boggess said.

Randall Parkinson, a coastal geologist focused on climate change adaptation at Florida International University, said the recommendations were likely to change how experts in south Florida are thinking about and proposing restoration projects. The assessment will go to the US Army Corps of Engineers and Interior Department and the South Florida Water Management District.

“Somehow, someone has to decide how much water will it take to get them back to being able to keep pace with sea-level and how do we monitor that to know how to change that over time, as may be necessary,” Parkinson said. “It would have been a huge challenge just to restore [the Everglades] if the climate and everything was in a steady state, but it’s not: it’s a moving target and it’s moving in the direction that increases the challenge.”