WILLISTON -- Vermont's first inhabitants used these waters.

Perhaps they fished Muddy Brook, stalked game on its banks or paddled its current to the Winooski River. They left records of their passing: Dozens of archaeological sites dot Muddy Brook's shores.

Muddy Brook was one of the first Chittenden County waterways mapped by Europeans in a 1794 survey. Later settlers put the brook to work. They built a sawmill and carding mill on the water, which today divides South Burlington from Williston.

Two hundred years later, Vermonters are still putting Muddy Brook to work. Instead of transporting native Vermonters to the Winooski, Muddy Brook carries a toxic load of chemicals, tons of sediment and pounds of heavy metals: Lead, zinc, copper and petroleum products lace its waters. Soil washed from new construction and eroded from tributaries cloud the brook.

Muddy Brook has seen more development than most Vermont streams -- and it shows. In its 20.8-square-mile watershed -- one-quarter of 1 percent of the state's land area -- Muddy Brook is home to roughly 5 percent of all of the state's stormwater permits. That includes the big box stores in Taft Corners.

The lower portion of the brook fails state standards, a problem that has won it a nearly permanent place on the state's problem river list.

This is a story about a polluted stream and how it got there. It's a story that's written in the alphabet of everyday life: Parking lots. Rooftops. Shopping malls. Cars.

And there is more to come. Developers are ready to build Maple Tree Place, a mammoth mix of office and retail development at Taft Corners. Its roofs will cover 12 acres of what is now meadow. Another 23.2 acres will be covered by roads and parking lots.

The story of Muddy Brook demonstrates the tremendous difficulty posed by stormwater runoff. It's a problem that plagues many small streams in suburban Vermont, but the problem, like water, moves downstream. The pollutants that foul Muddy Brook from stormwater eventually end up in Lake Champlain.

Falling short

Erosion and runoff from development in the watershed flush more than 60 tons of sediment into tiny Muddy Brook each year, the state estimates, as well as 300 pounds of phosphorus and 60 pounds of heavy metals.

That's in spite of the fact that the state has regulated stormwater for decades. Initially, the process was intended to protect neighbors from flooding. Stormwater permits issued since 1997 are supposed to clean up water quality, too.

Muddy Brook is prime evidence that the system is flawed, critics say. Just a handful of people police the state's 1,200 stormwater permits. State officials concede that's not enough, though they hope the combination of a new Vermont stormwater law passed in the last session and new federal stormwater regulations will improve matters.

Some environmental groups say the state has dallied too long. One group, the Conservation Law Foundation, says until the state requires everyone in a watershed to clean stormwater runoff, no new development such as Maple Tree Place should be allowed.

"We need to get all the polluters to the table, and figure out how to do the cleanup, and where to find the money,'' said Chris Kilian, with the Conservation Law Foundation. ''These costs should not be borne by the public at large. In the case of commercial developments, those costs should be (shouldered) by the people who are making money from those developments.''

Otters and Turkeys

Vicki Fraser knows a very different Muddy Brook. She lives not far from the brook's source in the wetlands around Shelburne Pond.

Fraser is co-chairwoman of the Friends of Muddy Brook, and for 13 years she has been watching from the window of her Van Sicklen Road home in Williston as a parade of wildlife uses the brook.

"We have a lot of wild animals,'' she said. ''Bobcat, wild turkey, mink, otter, deer, red foxes and even a bear has come through occasionally.''

The Muddy Brook that meanders past Fraser's house flows by a rich assemblage of flowers and frens. Mussels and clams live in the brook's bed. As it trickles past Fraser's home south of Interstate 89, Muddy Brook hasn't yet coursed past Chittenden County's retail-shopping mecca at Taft Corners.

Even where Muddy Brook runs under Marshall Avenue in Williston, with its smattering of warehouses and industrial buildings, residents love having the waterway as a neighbor.

Becky Bedard and her family live beside the brook off Marshall Avenue. She said her children catch fish and crayfish in the river, and the family watches otter, beaver and ducks in and on the water.

"I have been here three years now,'' she said. ''I have never known it to be dirty.''

The history

Muddy Brook won its name for a reason: The river has always carried more than its share of sediment from the erodible soils through which it carves.

Ever since the first farmer plowed a furrow along its banks, the river has felt the effects, says Jim Pease, non-point source coordinator for the state's water quality division.

This was in a degraded condition to begin with, from farm development,'' he said of the brook.

Vermonters have done far worse to Muddy Brook. One arm of Muddy Brook begins in a wetland and immediately disappears into a culvert for about 50 yards beneath Engineers Drive in Williston.

Pease doesn't know when this happened -- the state has regulated stormwater in some fashion since at least 1972 -- but he thinks it could have happened in the 1960s, during Chittenden County's first big growth spurt.

This is more than an aesthetic problem. A tributary that runs through a culvert is essentially dead. No fish can live in it, no bugs, no mussels or clams, no plants. Eventually, the loss of small tributaries affects the brook downstream. It's like cholesterol blocking an artery.

"We've lost this tributary,'' Pease said of the piece of Muddy Brook that has been paved over by Engineers Drive. ''And once you've lost the tributary, you see the stream start to degrade.''

Sediment and more sediment

Stuffing the brook into culverts gave way to a solution that was only marginally better. The state, until 1997, required developers to build structures that would tame runoff from excessive rainfall.

That's the guiding principle of the permits granted to most of the developments at Taft Corners. They control flooding but weren't designed to remove the quantity of sediments, toxics and nutrients needed to improve water quality.

Most systems catch water when it comes off a roof or parking lot, and pipe it to a pond with a drain that allows the water to siphon slowly out. There's a pond beside Wal-Mart.

The ponds are like giant bathtubs. They fill up until the water reaches a hole in a concrete pipe, and then the water drains slowly out. Eventually, the pond dries up until the next big storm.

The systems, once considered state-of-the-art, don't stop all the pollution stormwater can carry. Just one section of the Taft Corners Commercial Park drains nearly 13 tons of sediment into Muddy Brook each year, Pease has estimated, along with 30 pounds of heavy metals and 40 pounds of phosphorus.

By comparison, the Griswold Industrial Park downstream has no stormwater controls, according to state records. The park contributes 17 tons of sediment only 4 tons more than Taft Corners and 10 pounds more of heavy metals each year.

Disappearing fish

Pump enough sediment, nutrients and petroleum products into Muddy Brook, and you're bound to see the effects. The waterway runs thick and brown as a chocolate milkshake near the South Brownell Road overpass at Interstate 89.

Last year, the state uncovered an alarming trend in this stretch of water: the number and types of fish in the river plummeted.

Aquatic biologists ''didn't think it was related to the lack of rain,'' Pease said. For example, mud minnows had dropped out of the brook's population, he said, and white sucker and black-nosed dace were virtually the only types of fish in the stream. Both species are tolerant of pollution.

Small streams like Muddy Brook may sometimes experience dramatic natural shifts in populations, he said, but usually the fish populations bounce right back. For Muddy Brook, there has been no rebound.

"The trend is what we are concerned about,'' he said.

Protecting water quality

Since 1997, the state has required new developments to build systems that take pollutants and nutrients out of the stormwater as well as prevent downstream flooding.

The strategy is applauded in theory by environmentalists and natural resource managers. It can be done by building artificial wetlands or other vegetated barriers that both slow down the flow of stormwater and filter nutrients and sediments from the water

It's an imperfect approach. The state has just a handful of inspectors to make sure stormwater controls are in place and working, which is totally inadequate, said Bob Kort, a stormwater expert with the Natural Resources Conservation Service.

For example, The Miller Group built a 207,000-square- foot warehouse off Marshall Avenue in Williston last year, with state-of-the-art stormwater and construction erosion controls. Yet silt fences around the warehouse have been swallowed by sediment.

Owner Robert Miller, who wasn't aware there was a problem, said he would fix the silt fences. "We take this seriously,'' he said. ''But it is hard to predict (if the fences will fail). ... We have had a lot of rain, but that is no excuse.''

Kort and others say the state ought to require older developments to improve their stormwater controls. One way to do that, he said, is to require new developments to pay for upgrading older developments.

"It will be tough to sell something like that,'' he said.

The state is already testing this approach with developer Jeff Davis and the Taft Corners Commercial Park. Davis will be required to upgrade the stormwater system if he adds significant businesses, said Randy Bean, with the state Department of Environmental Conservation.

The Conservation Law Foundation's Kilian said the state has moved too slowly. Until the state moves more aggressively to protect small streams, he said, development ought to be halted in streams where water quality has been fouled by stormwater.

"Whether it is Maple Tree Place or some other big box or mall, somebody has got to step in and make this point,'' he said.