SOUTH FLORIDA -- Budget cuts at both the state and federal levels will reduce scientists' ability to monitor the health of Florida Bay as well the effects of Everglades restoration projects on the shallow 850-square-mile estuary.

"We had to make some tough choices," said David Tipple, the chief of Everglades restoration monitoring and assessment for the U.S. Army Corps of Engineers.

The cuts will affect a wide range of scientific efforts in the bay. Water quality monitoring that commenced in the late 1980s will be eliminated. So will the tracking of juvenile pink shrimp in the shallow-water estuaries of Florida Bay, Biscayne Bay and 10,000 Islands region.

Sampling of food sources that sustain the prized roseate spoonbill have also been slashed.

The cuts, by the Corps and the South Florida Water Management District, come as the two partners in the $20 billion Comprehensive Everglades Restoration Plan face belt-tightening measures imposed in Tallahassee and Washington.

The Corps will spend $2.8 million on Everglades-wide science monitoring this year, down from $5.5 million last year, Tipple said.

The South Florida Water Management District, obligated by Gov. Rick Scott and the Florida Legislature to cut spending by 30 percent, is going even deeper. The district will reduce its Everglades-related monitoring expenditures by 72 percent, from $2.3 million to $646,000, records show.

"The take home is it's the eyes of restoration," said FIU ecologist Joe Boyer, who oversaw water quality monitoring in Florida Bay until 2008. "You poke out the eyes of restoration, you're not going to be able to know what affect the stuff you are doing on land has on the receiving waters."

The elimination of the water monitoring program might be the most noticeable of the cuts to the bay science program. Until 2008, Florida International University monitored 28 sites in the bay for measures such as salinity, nutrients and chlorophyll -- the telltale sign of an algae bloom.

The program was cutback to 15 sites in the past three years and its management was transferred to the water district. The program's elimination would have placed a higher priority on the 40 water monitoring stations that NOAA oversees in Florida Bay. But the funding for that program, which currently comes from BP payout funds, is set to expire in February, said Chris Kelble, the NOAA researcher who compiles data from the sites.

That would leave the bay with only the four monitoring stations maintained by Everglades National Park.

The timing for the cuts is especially bad, Kelble said, because a key restoration project designed to divert water away from extreme South Florida's most prominent canal, called the C-111, and toward the bay, is nearly complete.

The losses will also make it harder to track algae blooms, said Carol Mitchell, Everglades National Park's deputy director of science.

"We are probably going to be less able to analyze the source and the causal effect of any bloom that we have," she said.

The loss of juvenile pink shrimp monitoring will also be felt, said Joan Browder, who runs the program for NOAA Fisheries Service.

For one, the data it provides can be useful in managing the valuable commercial species. But the information also has broader applications, according to Browder. That's because the pink shrimp population is indicative of the health of the bay in general, Browder said. When clean and ample freshwater are flowing into the bay, the pink shrimp flourish. When the bay is overly salty, they struggle.

Spoonbills, whose foraging is heavily reliant on the normal summer/wet, winter/dry pattern of the Everglades is viewed as an indicator species as well. But with a funding cut of 36 percent in store for the coming year, Audubon of Florida plans to sample just nine of the 19 spoonbill foraging grounds that it sampled in previous years.

"It just reduces the power of what I have and what I can say about the health of the Everglades," Audubon's Jerry Lorenz said. The cut forced two lay-offs at Audubon's Tavernier office. "That health means the fishing industry, the boating, the diving industry," Lorenz added.

Some of the Florida Bay programs were spared the scalpel, however.

No cuts are being made to a program that monitors Florida Bay juvenile sportfish.

And while 36 percent less will go to seagrass monitoring, the cut won't impact the program's core missions of charting seagrass coverage and recording the types of seagrass in each area.

"We kind of lost some bells and whistles is what we lost," said Penny Hall, who runs the program for the state's Fish and Wildlife Research Institute.

The Army Corps' Tipple said that under difficult circumstances the agency tried to make cuts that would do the least harm. The choices of what to cut, he added, were made only after consulting with the research scientists.

Still, Tipple acknowledged that with less scientific monitoring it will be harder to determine cause and effect as Everglades restoration moves forward

"It will increase our risk and uncertainty in certain areas," he said.

rsilk@keysnews.com