Scientists have developed a new technique to answer a fundamental, yet maddeningly complex question: Is the amount of nitrogen and phosphorus reaching the Chesapeake Bay trending up or down?

About 30 billion gallons of water a day flow into the Chesapeake from its major tributaries. The amount of nitrogen and phosphorus along for the ride varies, based on a host of factors such as the volume of river flow, the season or changes on the land.

Even short-term events make big differences. Melting snowpacks can release a surge of nitrogen, while pounding thunderstorms effectively scour phosphorus from land surfaces and stream banks.

Sorting through the variation and finding a trend has eluded scientists. A number of methods have been used over the years, and each had shortcomings.

Now, a new method that takes better accounts of variations in streamflow, seasonality and the impact of human activities such as wastewater treatment plant upgrades, is providing a more refined - and complex picture - of what's coming downstream.

Bob Hirsch, the USGS scientist who developed the new analysis technique, and his colleagues, Douglas Moyer and Stacey Archfield, examined 31 years of data - from 1978 through 2008 - collected at the USGS' nine river input sites that surround the Bay. Because all of the sites are located just upstream of the head-of-tide, they capture information about the nutrients and sediment reaching tidal waters from the Bay's nine largest rivers.

The information contains good news and bad.

During that 31-year period, there were substantial downward trends in the amount of nitrate flowing into the Bay from the Pamunkey and Patuxent rivers. There was a substantial increasing trend in the Choptank. The other rivers - Susquehanna, Potomac, James, Rappahannock, Appomattox and Mattaponi - did not have substantial trends (defined as an average rate of change greater than 1 percent per year either up or down).

With phosphorus, Hirsch found a substantial downward trend in the Patuxent, and substantial upward trends in the Rappahannock and Pamunkey over the three decades. Other rivers did not have trends greater than 1 percent per year for the period.

The analysis also showed that different trends emerged when looking at specific time periods.

For example, data from 2000 to 2008 show a different picture. In the more recent nitrate data, the Potomac, Patuxent, Pamunkey and Appomattox rivers all show substantial downward trends. The Susquehanna, the Bay's largest tributary, also shows a strong downward trend of slightly less than 1 percent a year during that period.

But the James and Choptank rivers show substantial increasing trends, with nitrogen levels increasing an annual average of 1.6 percent on the Choptank and 1.2 percent on the James.

The story for phosphorus is more disappointing. More than half of the tributaries - the Rappahannock (up 8.4 percent a year), James, Susquehanna, Choptank and Pamunkey rivers - are showing substantial increasing trends since 2000.

Only the Potomac has a downward trend for phosphorus in the last decade, decreasing an average of 2 percent a year.

In addition to the information on the rivers, another big piece of information was perfectly clear: Change in most of the Bay watershed is very slow.

"Things are gradual," Hirsch said. "It took us at least half a century, if not a century getting into the bad situation we are in today. It is going to take similar amounts of time to get out of it, as far as I can see. It doesn't mean don't try, it means be patient."

Over the years, scientists have developed a number of techniques to "flow adjust" to detect nutrient trends hidden within the widely variable fluctuations of precipitation and river flows. By removing the influence of flow, scientists can better understand whether actions to reduce pollution are effective.

Previous techniques used smaller data sets for shorter periods of time. They were less capable of capturing some of the substantial changes that were taking place in some of the watersheds. The new technique uses large monitoring data sets (more than 13,000 water quality measurements and more than 100,000 daily river flow values) to represent the changes in the behavior of watersheds.

Disproportionately high amounts of nutrients move downstream during high river flows and severe storms. Thus, a year with very high streamflows can lead to a conclusion that conditions are getting worse. The new method uses a technique that accounts for the influence of these year-to-year flow variations while still allowing the analysis to show the true underlying change in the behavior of the watershed.

The results can be revealing.

On the Patuxent River, all major wastewater treatment plants underwent upgrades in the 1980s and early 1990s. During low flows, when discharges from those plants make up most of the water in the river, past monitoring analysis showed that phosphorus declined sharply overall since the 1980s.

But when the effect of storms is factored in using the new techniques, phosphorus levels are showing a slight increasing trend, apparently reflecting the increased influence of runoff in the watershed.

Conversely, on the Choptank, the rate of increase in nitrogen runoff has slowed a bit in recent years. But the amount of nitrogen seen is increasing during periods of low flows, which are dominated by groundwater discharge.

Hirsch said the new analysis provides clues as to what is going on in each watershed.

"In the Choptank, clearly, increased nitrate in the groundwater is leading to increases in the amount of nitrate flowing to the Bay," he said.

That could mean that actions to control runoff into surface streams are simply diverting nitrogen to groundwater, where it will still reach streams, but often not for years.

"We can see some of these patterns much more clearly than before with this analysis," said Bill Dennison, a scientist with the University of Maryland Center for Environmental Science who oversees production of an annual Bay report card. "This is a big step. It has been important to do, and do well. And it's something that we've needed for a long time."

Scott Phillips, Chesapeake Bay coordinator for the USGS, said about 30 monitoring locations throughout the watershed have enough information to allow the use of Hirsch's data-intense analytical technique. The USGS hopes to begin showing results from those sites next year.

Within the next few years, the data will be used to show how close rivers are to meeting their nutrient reduction goals.

"Up to this point, most of the estimates of progress in nutrient reduction are based on modeling results," Phillips said. "This would provide another really important piece of information - based much more directly on actual river monitoring data."

The findings differ from computer model projections used by the EPA to set cleanup goals and assess progress toward meeting them. The model indicates downward trends in all rivers, and in some cases, much larger trends.

Part of the difference is that monitoring sites capture only a portion of the drainage area of river basins, rather than the entire basin, because streamflows cannot be monitored in tidal portions of rivers. And the model predicts future nutrient reductions based on getting immediate benefits from management actions - but it can take years for nutrient reductions from cover crops or forest stream buffers to be fully realized, something often referred to as a "lag time."

Still, the lack of trends in monitoring data after more than two decades of nutrient reduction efforts in some rivers, and the reversal of downward trends in others, is troubling.

One site of particular concern is the Choptank River. The increases monitored there were found despite ramped-up efforts to control agricultural runoff in the last two decades. The USGS monitoring site only captures a portion of the drainage basin, but most of it is forest or agricultural.

The findings come as no surprise to Tom Fisher, a scientist at the University of Maryland Center for Environmental Science's Horn Point Lab who has been monitoring 15 agricultural subbasins and two forest subbasins in the Choptank watershed for years.

"We don't see any positive trends in those," he said.

Part of that may be attributed to lag times, but Fisher said the lack of trends most likely means that not enough runoff control measures have been implemented on the land to affect water quality. He and others also believe that many agricultural control techniques, typically called best management practices or BMPs, are probably not as effective as people believe or may not be fully implemented.

"They have done things on the land, some of which may have helped," Fisher said. "But I think some of their estimates of how much they helped are way too optimistic. No one has tested most of these things at the watershed scale."

Most studies of BMP effectiveness stem from small, carefully studied plots. But their actual effectiveness can carry widely.

New insights about their real-world effectiveness may be on the way. As part of the new federal executive order strategy, the USGS next year plans to begin monitoring five small watersheds to better understand whether on-the-ground actions are having the anticipated impact on nutrients reaching the stream.

Three of the sites are in priority watersheds identified by the U.S. Department of Agriculture for more intense efforts to promote best management practices among farmers. The USDA will also step up farm monitoring to ensure BMPs are implemented and to account for other actions that may influence nutrient trends.

The goal of the new, small-watershed monitoring project is to see whether intensified actions on the ground can move the needle on stream water quality.

The answer won't come soon. Because of lag times and natural streamflow variations, Phillips said it will take five to 10 years to have clear results.

"That's the tyranny of monitoring," Dennison said. "You have to be patient and wait. But we need to do a better job of understanding which best management practices are clearly making a difference and figure out how to emulate those successes."

Monitoring also provides a reality check for what is happening on the watershed - and for policy decisions. In recent months, officials from most Bay states have argued they have implemented more agricultural best management practices than are credited in the computer models used by the EPA to estimate cleanup progress. But data from the Choptank and other rivers suggests that any additional actions taken on the land often are not being seen in the water.

"It makes you wonder whether all of the funded and all of the voluntary BMPs that are purported to be on the ground are actually on the ground," said Kevin Sellner, executive secretary of the Bay Program's Scientific and Technical Advisory Committee, which recently produced a report advocating more small watershed monitoring.

In addition to its stepped-up monitoring, the USGS will also be summarizing results from existing studies to try to provide managers with more immediate insights on the effect of BMPs in agricultural, suburban and urban areas.

It's critical information because, ultimately, when it comes to the Bay, it is the monitoring data that has the last word. The Chesapeake can only be removed from the EPA's list of impaired waters when it meets water quality standards in the real world - not in model projections.

"Sometimes people lose sight that our final measure is monitoring in the Bay," Phillips said. "Up to this point, most of the progress is based on modeling. This new technique provides another really important piece of information to show progress toward reducing nutrients in the watershed, along with using tidal monitoring data to assess progress toward improving dissolved oxygen and water clarity in the Bay."

But the data indicate that the monitoring won't render a final verdict for a long time.

The EPA is developing a new cleanup plan, called a Total Maximum Daily Load, that requires all actions needed to achieve a clean Bay be implemented by 2025. But officials have cautioned that because of lag times and natural variations, the actual clean Bay won't be realized for years after that date.