SIOUX FALLS -- The Big Sioux River snakes 420 miles down eastern South Dakota.
From its headwaters in Roberts County, it gradually drops 800 feet as it cuts through the Coteau des Prairies flatiron and meanders into Iowa and flows into the Missouri River.
Some of the state's largest cities were built along its banks -- Sioux Falls, Brookings, Watertown -- as people and industry flocked to the wide-open prairie. Farms, feedlots, cities, industry all thrive, each dumping the fruits of their progress into the river.
Only in the past half-century has concern about the environment stirred up political pressure to do more to preserve the health of the watershed. Riverside communities began viewing the Big Sioux as something more than a semi-regulated dumping ground.
Now, the river is listed as the 13th dirtiest in the nation, by one measure.
"We're recognizing that, if we ruin it, it's not going to be there for our children," said Barry Berg, who coordinates the watershed cleanup program for the lower stretch of the river.
New laws placed long stretches of the river on a list of federally impaired waterways. But despite years of clean-up efforts -- millions spent on programs to help rural landowners fence off cows, feedlot owners to invest in animal waste-control systems, industrial and municipal plants to upgrade their equipment -- little has changed.
In places where water-quality officials have determined the river should be clean enough to swim in, it's not, even as cities such as Sioux Falls bank their growth on the river as a source of recreation and entertainment.
Part of the cleanup process involves identifying the causes of the pollution, a process in which figures a familiar tension of upstream versus downstream interests, urban polluters -- which typically are regulated point sources -- versus rural, which typically are not. A longstanding aversion to regulation in South Dakota hampers cleanup, some contend.
Given the slow pace of improvement on the river, people are left with two options, said Jay Gilbertson, manager of the nine-county East Dakota Water Development District: Either regulators need to be empowered to take a harder line on nonpoint sources, or "we need to take a more realistic look at how the river is used."
"At the end of the day, the only real metric is the quality of the water," he said. "That's what starts the whole thing in the first place. If we truly believe that the Big Sioux River from Dell Rapids south ought to be swimmable, then we're going to have to do something more than hope that people will voluntarily change the things that they're doing."
But that will require changing the way people farm and how industries do business. If history is any guide, change will be slow.
Sioux Falls has spent millions of dollars developing the downtown River Greenway project. In recent years, it has put in two new canoe launches, though much of the river does not meet the standard for limited-contact recreation.
"It's been in my lifetime that Sioux Falls has realized it has an asset in the river, that it could be used for entertainment and recreation, not just industry," said Mary Finck, who grew up in the area and paddles with the South Dakota Canoe and Kayak Association.
Nancy Gellerman, who owns the Wild Sage restaurant at Cherapa Place downtown, said the river gives the downtown development "a great energy," regardless of what's in it.
"To be in the river -- that's not the appeal," she said. "The appeal is being on the river. Unless you live in Alaska and have glacier-fed water, it's going to brown or green."
No matter the color, Mayor Mike Huether said the river matters.
"Striving for clean water is the proper thing to do, no matter if it is the Big Sioux, the Mighty Missouri or a stock pond on someone's farm," he said. "More and more people will enjoy the Big Sioux and our greenway, so any efforts to make it more vibrant are good investments."
Forty years ago, researchers at Sioux Falls College embarked on a study for the National Science Foundation that became perhaps the first attempt to gauge the river's health.
They found extensive nutrification and concentrations of bacteria thousands of times greater than prevailing water quality standards, a pollutant load that intensified significantly downstream of Sioux Falls. The city wastewater facility and the John Morrell & Co. meatpacking plant were assigned most of the blame.
The study was released the same year the Clean Water Act was signed into law. It was key legislation that, among other things, requires states to regularly measure and rank the health of their waters.
Year after year, long sections of the Big Sioux and its tributaries are listed as "nonattaining" the standards that guide their uses. By one crude metric -- total pollution by weight -- the Big Sioux is the 13th dirtiest river in the country, according to the advocacy group Environment America.
Since the 1980s, when the state began gathering robust water quality data, monitoring shows little change on the river, said Sol Brich, watershed coordinator with the South Dakota Association of Conservation Districts. He used to help write the state water quality reports. In one sense, he said, this is a positive sign, considering the population growth in eastern South Dakota and the amount of new cropland that's been put into production.
Some areas of the river have improved; some haven't. Better conservation practices have reduced erosion levels on the heavily farmed tributaries, for example, Gilbertson said. But bacteria problems persist.
One reason is that pollution standards are higher below the Moody County line, where swimming becomes one of the river's designated uses. One criterion for a river to be swimmable is that it can't have more than 400 colonies of fecal coliform per 100 milliliters; the stretch through Sioux Falls has struggled for years to meet that standard.
In the past, the river also has been impaired with regard to ammonia, dissolved oxygen and iron, said Bob Kappel, environmental manager for the city of Sioux Falls.
"Decades ago, they didn't have the monitoring capabilities that they have now," said Kappel, who has worked at the city for 27 years. "But obviously, the Big Sioux River was in much poorer quality before the Clean Water Act was passed."
In Sioux Falls, the city wastewater plant and John Morrell are the two major point sources that discharge into the river; municipal storm-water runoff also is monitored and regulated, said Kelli Buscher, surface water quality engineering manager for the South Dakota Department of Environment and Natural Resources.
Sioux Falls has spent millions to upgrade its sewers after being overwhelmed by heavy rains in 2010, leading to a system failure that dumped 65.3 million gallons of raw and partially treated sewage into the river. The city was fined $10,877.
For rural landowners, this really "dumped salt into the wound," said Jack Majeres, chairman of the board of Moody County Conservation District, lead agency on the Central Big Sioux Watershed Project.
"Granted, the city got fined and everything else," he said, "but the rural producers are saying, 'Why are you pointing the finger at us?' "
Morrell also has been in trouble with the state. It was fined $44,079 in October following three years of effluent violations that, at its peak, saw the plant discharging three times its permitted limit of ammonia into the river.
Dennis Treacy, chief sustainability officer for Smithfield Foods, Morrell's parent company, said the plant is installing the upgraded equipment required by the state compliance order. He added that all Smithfield companies share a corporate ethic to abide by environmental laws and reduce pollution loads.
"I'm optimistic that we're on the right track," he said. "We certainly are going to comply with the law, and we're complying with the consent order. The improvements that are included in there are expensive, but we understand our responsibility, and we'll do it. (Environmental protection) is something we think about daily."
When operating within their permits, Buscher said, neither Morrell nor the city discharges concentrations of pollutants at levels that impair the river. "The Clean Water Act has been effective at controlling these point sources," she said.
Morrell was the only source of pollution on the Big Sioux listed in the Environment America report, which compiled data from the Environmental Protection Agency's 2010 Toxic Release Inventory (TRI). The TRI database tracks self-reported releases of some point-source chemical discharges.
Morrell, which butchers and processes around 17,000 hogs daily, was No. 11 on the report's list of TRI facilities that discharge chemicals into the nation's waterways - mostly nitrates from the chemical breakdown of ammonia in pig blood. Nitrates can be harmful in high concentrations if found in drinking water. But the water below Morrell isn't used for drinking water.
Though Morrell sent a nitrate load of 2.95 million pounds into the river in 2010, downstream sampling has shown nitrate levels within normal ranges.
"(TRI) is easy picking for an activist group, what seems to be a ranking for big polluters," Treacy said. "All of the action on pollution control in this country is on concentrations."
The bigger concern is what happens farther downstream. The Big Sioux drains into the Missouri River, which drains into the Mississippi River, which empties into the Gulf of Mexico, where all of the nutrients picked up along the way are deposited. Excessive nutrient loading has fed a dead zone in the coastal waters that's now about the size of Lake Ontario.
Researchers have linked these nutrient loads to farm runoff from predominantly agricultural watersheds such as the Big Sioux.
Gilbertson said his staff did some back-of-the-napkin calculations a few years ago to get a rough picture of the sources of bacteria in the watershed: Municipal wastewater plants accounted for less than 1 percent; animal waste, 5 percent at the outside; home septic systems, in the unlikely event that all of them suddenly began straight-line failing into the river, 20 percent. The rest was agriculture.
"It's not an indictment of livestock," he said. "It's a recognition that that's what happens in the Big Sioux basin. We raise cows. We use manure for fertilizer."
Wayne Smith, director of field services at South Dakota Farm Bureau, said every polluter on the river - urban and rural, point and nonpoint - can do better.
"Agriculture has been there forever, basically," he said. "They've been there as long as the city of Sioux Falls. I think we both can improve the management techniques, and I'm encouraged by what we've accomplished over the last 20 years."
French traders may have mapped the Big Sioux River as early as the 17th century. In an 1804 journal entry about "the Soues River," William Clark noted that "below the falls a Creek Coms in which passed thro Clifts of red rock which the Indians make pipes of."
Forty years later, French cartographer Joseph Nicollet wrote about a river the natives called Tchan-kasn-data ("thickly wooded river") or, in its upper reaches, Watpaipak-shan, the crooked river.
"It flows through a beautiful and fertile country; amidst which, the Ndakotahs, inhabiting the valleys of the St. Peter's and Missouri, have always kept up summer establishments on the borders of the adjoining lakes, whilst they hunted the river banks," he wrote. "Buffalo herds are confidently expected to be met with here at all seasons of the year."
Early white settlers saw the river as a potential source of power for industry and as a liquid conveyer belt for carrying away waste. Throughout the 19th century, people commonly dumped raw sewage, industrial waste and dead animals directly into the river.
"But, of course, you always dumped it downstream from where you were," said Bob Kolbe, president of the Minnehaha County Historical Society.
About the time Sioux Falls began treating its wastewater, Seney Island, a popular picnicking excursion north of the falls, was filled in to accommodate expanding downtown industry. Subsequent investigations have found harmful compounds such as lead and battery acid in the garbage that had been used as filler, Kolbe said.
Upstream, meanwhile, the government was encouraging farmers to build feedlots on steep slopes that drained directly into the river.
"Back in the '50s, Extension - that was their philosophy: Get it on a slope so you don't have to mess with all that manure," Majeres said. Advice now is contrary to that.
Smith of the Farm Bureau said no one involved in agriculture "is out here to pollute."
"I'm not saying farmers and ranchers have the right to pollute," he said. "They don't. They're doing things the same way they did them 35, 40 years ago. But we are taking a good, hard look at updating some of those practices."
With the shift in cultural values that accompanied passage of the Clean Water Act came a period of regulation by litigation. Environmental groups went state by state suing the federal government to enforce clean water laws more aggressively.
South Dakota's turn at litigation came in the mid-1990s in a case that marked a shift in the state's enforcement culture, Gilbertson said. Before, officials would wait for local residents to identify a problem before initiating a cleanup plan.
"The EPA and the state hadn't really been taking a terribly aggressive role," he said.
The case was settled in 1999 after the state drew up its first list of impaired waters. For each waterway on the list, the state was required to create a daily load plan - a calculation of how much pollution a body of water can accept and still meet water quality standards.
"In '98, every water body that was impaired became a target," Gilbertson said. "And if it didn't have a natural constituency, that's when East Dakota got involved. ... The size of the projects grew substantially."
Regulators began taking a system-wide approach to cleaning up the river, using newly available federal dollars to run baseline studies and develop watershed remediation projects.
Water quality rules are beginning to percolate down to the county level. Many counties now are adopting their own guidelines for animal feeding operations, Brich said. He sees that as an encouraging sign.
"That's how you see that the public has direct input into the process," he said. "You have these federal laws, but it all comes down to local action. When you start seeing a county adopting ordinances that affect how business is done in that county, and it's driven by water quality, then you know the public is involved."
To address nonpoint pollution, the Big Sioux was divided into three large assessment projects - upper, central and lower - and each of these was divided into a few dozen segments of river. If enough samples in an area exceeded the standards, "it was a suggestion there was a problem," Gilbertson said.
Among the first tasks for project coordinators was to gather enough data to assess progress. It is too expensive to sample continuously all the way up and down the river, Majeres said, and several years of data are needed for useful conclusions.
When reporting their progress to the EPA, coordinators rely mainly on engineering models to estimate load reductions, Brich said.
Buscher said better data is needed to quantify the sources and extent of nonpoint-source pollution on the Big Sioux. Smith of the Farm Bureau said "it's still wide open as to what the root causes are" of nonpoint-source pollution, and so he favors keeping the voluntary, incentive-based approach to controlling agricultural runoff.
"There needs to be caution in being able to identify the exact source," he said. "Sometimes we jump to conclusions."
Officials in the nonpoint source programs began narrowing their focus about seven years ago to work with landowners in the river corridor.
They're also creating a market for water quality credits. Cities struggling to hit water quality targets could buy credits from upstream farmers, who would generate credits by investing in projects that improve the river.
"We're cutting a new path here," and it's further evidence of a new level of city-country cooperation, he said. Sioux Falls used some of its state revolving fund money for nonpoint projects upstream rather than infrastructure upgrades, for instance.
"It's that cooperative effort we're trying to pull together," Majeres said. "Everybody has a stake in making this project successful. It isn't one segment over another that's more at fault. We all have to take ownership in this."