For the third straight year, wading bird breeding was down in the Everglades.

Nesting numbers, considered an important measure of the health of the overall system, fell by 39 percent compared to average activity over the past decade, according to an annual survey compiled by the South Florida Water Management District.

The drop-off wasn’t as disastrous as in decades past, but it continued a relatively poor trend since an encouraging breeding frenzy in 2009, when white ibises, wood storks, great egrets and a handful of other key species produced more than 77,500 nests — the biggest season since the 1940s. The 26,395 nests estimated last year were almost the same number as in 2011, and a slight increase from 2010.

Mark Cook, the water district’s lead scientist for Everglades assessment, said swings in seasonal water levels are mostly to blame for inhibiting breeding in a sprawling system that has been shrunk and strangled over the past century by development, roads and drainage canals.

Back-to-back drought years reduced the numbers of tiny fish that provide food for many birds. Then, in the prime nesting month of April, untimely storms disrupted seasonal drying cycles that concentrate fish and other tiny prey, which wading birds depend on to feed their fast-growing and voracious chicks.

As rising waters disperse prey, Cook said, “the parents are just unable to keep up with the demand,” and many chicks don’t survive.

Environmentalists said the recent dips after a decade of generally rising nesting point to the need to move forward on Everglades-restoration projects.

Some species, such as the wood stork and tricolored heron, suffered worse drops than others.

The population of wood storks, long classified as an endangered species, has expanded across the southeastern United States to the point that federal wildlife managers last month proposed proposing reducing its status to the less-severe “threatened” category. But for the fifth time in the past six years, there were no wood storks nesting in what once was the largest breeding colony in the United States — the Corkscrew Swamp Sanctuary in Southwest Florida.

Jason Lauritsen, director of the Audubon-managed Corkscrew sanctuary, said the storks’ disappearance from a prime breeding ground points to a troubling disruption of seasonal cycles that flood and drain marshes that are critical to wading birds.

“If we hope to recover the largest historic colony in the U.S., immediate focus must be put on restoring and protecting short-hydroperiod wetlands in the western Everglades,” he said.

While breeding has crept up in Everglades National Park, once home to about 90 percent of wading bird rookeries in South Florida, Audubon points out that the number still falls far short of restoration targets.

Cook agreed that the $12 billion Everglades restoration effort should ultimately reduce extreme swings that have been exacerbated by an antiquated flood-control and water-storage system.

But even the unspoiled Everglades was a boom-or-bust system tied to South Florida’s shifting weather patterns. Birds begin breeding as water levels fall, so rainfall timing and volume are a key to their success.

In the 1900s, the wading birds of the Glades were almost blasted into oblivion by plume hunters cashing in on a craze for feathered hats. By the 1930s and ’40s, after a public outcry brought a crackdown on hunting, breeding rebounded, resulting in 35,000 to more than 200,000 nests each year.

But after the ’40s, drainage canals, flood-control levees and rampant development reduced the historic Everglades by half, cutting populations of the nine surveyed species by an estimated 70 to 90 percent. Poor water-management practices helped drive the number of nests to a low of just 5,000 in 1983 and 1985.

There have been occasional upticks — more than 50,000 total nests in 1972 and 1992 — but it has only been over the past decade or so, with improved water management practices, that the trends began steadily improving. Some birds, however, continue to struggle for reasons that Cook said are not well understood, including the snowy egret and tricolored heron.

On the plus side, droughts appear to spark the bird booms, with exceptional nesting years occurring two years later. The prevailing theory, said Cook, is that the dry spells knock back populations of large fish that feed on crayfish and smaller fish that make up many birds’ primary diet. When the water comes back, the plentiful prey help power the avian sexual surge.

After a healthy rainy season last year, many marshes across the Glades appear to be full of birds. If the typical drying patterns prevail into early spring, the birds could be back on their games this year, Cook said.

“It all looks good at the moment,” he said.