The James River poses one of the most perplexing cleanup challenges in the Chesapeake Bay watershed, according to researchers who have attempted to unravel its mysteries.The alga (Margalefidinium polykrikoides ) blooms in the James River near the Monitor Merrimac Bridge in August 2013. (Wolfgang Vogelbein / VIMS)

Its tidal waters range from nearly as salty as any ocean to as fresh as any inland lake. Its many twists and turns slow downstream flow to a crawl, providing a potential breeding ground for harmful algae blooms. And its shallowness only ensures that those blooms are never far from the sunlight they need to explode.

“It’s like a perfect storm there for algae,” said Tish Robertson, an assessment coordinator with the Virginia Department of Environmental Quality.

But figuring out the acceptable levels of algae — enough to help feed fish but not cause water quality problems — has proved to be a daunting task that has gone on for more than 15 years. It’s closely intertwined with determining the acceptable levels of nutrients, which feed algae blooms, that can go into the James.

Now, Virginia officials have emerged with adjusted criteria and a proposed regulatory framework to address concerns over algal growth. The proposal allows for some cases in which nitrogen and phosphorus — which feed the algae blooms — can exist in the river at higher levels than those set by the 2010 Bay cleanup plan, but are more in line with earlier estimates.

As a result, the new regulations could save wastewater treatment plants and other large polluters hundreds of millions of dollars in costs tied to upgrading their nutrient-removal technology. But those involved with creating the plan say it will still reduce algae blooms and their harm to the ecosystem.

“It is counterintuitive,” said Jamie Brunkow, riverkeeper for the James River Association. But his organization and many other environmental groups are nonetheless lining up to support the new framework, save for a few tweaks.

“I’ll admit it’s quite complicated. It’s hard to communicate with the public,” added Brunkow, a member of an expert panel that helped shape the proposal. “It’s not really a winners or losers kind of thing. It’s a consensus process. We had to all agree this is the right approach.”

The history of the problem is complex. The state in 2005 developed criteria for chlorophyll — a measure of algae growth — that would require additional nutrient reductions in the river. Then, in 2010, when the U.S. Environmental Protection Agency put forth its Bay cleanup plan, the Chesapeake Bay Total Maximum Daily Load, it estimated that even greater nutrient reductions would be needed  — a conclusion that raised immediate calls for more study.

The result was a 70-page report, which Brunkow said represents “a realistic and scientific path to get to a restored James River.”

The report stemmed from a $3 million, state-led study that took six years to complete and the development of a complex new computer model to better simulate the James’ unique conditions. The work led to a revised set of limits on the acceptable amount of chlorophyll in the river.

In what would be the first update to the chlorophyll caps since they were established in 2005, the DEQ is proposing that eight of the seasonally averaged concentration levels be lowered and two be raised. The limits vary by season and river segment. Regulators also created separate criteria that would apply to durations of one day for certain segments and one month for others.

The new criteria overall are more stringent, but the new rules would allow them to be exceeded more often. The net effect would still require wastewater treatment plants and industries to reduce their nutrient discharges, but by smaller amounts than the Bay TMDL had estimated.

If they take effect, the new criteria would require roughly three dozen affected dischargers on the river to spend about $250 million for upgrades instead of the nearly $950 million previously anticipated, according to state economic forecasters.

Before the study began, “we really didn’t have a strong science guiding what too much algae is,” Robertson said. “We feel like we have a more-sound basis for the criteria than what we had in 2005.”

The chlorophyll standards are receiving mostly positive reviews from wastewater officials.

“The science that has been brought to bear on this topic has just been tremendous and impressive,” said Jim Pletl, head of water quality for the Hampton Roads Sanitation District, which operates seven of its 16 southeastern Virginia plants on the Lower James.

The proposal could go before the Virginia Water Control Board as early as this summer. If the board approves the measure, Gov. Ralph Northam and the EPA would have to sign off before it takes effect.

The James is the only Bay tributary to have a specific numerical limit for chlorophyll except for tidal portions of the Potomac and Anacostia rivers within the District of Columbia. A “narrative” limit has been in force for other areas of the Bay since 2003.

Why the different treatment for the James?

The nutrient reduction goals for most waterways in the Chesapeake watershed were based on what was needed to reduce algae growth in order to relieve oxygen-starved “dead zones” in the Bay itself. But that is less of a factor for the James, experts say, because it empties near where the Bay meets the Atlantic Ocean. Its water quality has relatively little bearing on the Bay’s health.

Instead, its nutrient reduction goals were based on chlorophyll targets aimed at improving aquatic life in the river itself, said John Kennedy, director of the DEQ’s office of ecology. The metrics included water  clarity, acidity, the abundance of harmful algae bloom species and dissolved oxygen.

The 2005 regulation was underpinned, in some cases, by “best professional judgment” about the interplay between the James’ nutrients and algae, Pletl said. Little was known at the time about how an uptick of nutrients would affect chlorophyll levels and, in turn, how to link a rise in chlorophyll to ecological damage, such as fish kills and toxic algae blooms.

“Chlorophyll itself is not a toxicant,” Pletl said. “Making that link back to actual impact to populations and aquatic species is much more difficult.”

The new limits reflect improvements in modeling technology and a greater scientific understanding of the river’s plants and creatures, said Carl Hershner, director of the Center for Coastal Resource Management at the Virginia Institute of Marine Science.

“It’s really encouraging that both DEQ and EPA were willing to look at this issue and realize there was the potential for something unique,” Hershner said. “It’s a sign of the increasing sophistication of our water-quality management efforts.”

The James River carries water from as far away as the Appalachian Mountains and delivers it nearly 350 miles downstream to the Chesapeake Bay. The new chlorophyll measures target the 110-mile tidal stretch below Richmond.

Algae blooms are common, particularly in the Hopewell area, from May to September, scientists say. The blooms often produce microcystin, the same toxin that forced Toledo, OH, to temporarily shut off its water intake from Lake Erie in 2014.

The James’ tidal flow ensures enough mixing in the water column to tamp down toxins. But even if no toxins are present, algae can upend an aquatic ecosystem.

In response to the 2005 chlorophyll criteria, the state began requiring large polluters along the river to scrub more nutrients from their discharges. That led to at least $400 million in investments to jump-start the cleanup. So far, the James River cleanup accounts for 65 percent of the statewide reduction in nitrogen and 60 percent of its reduction in phosphorus from so-called “point” sources, according to a recent state tally.

The DEQ’s Robertson said those upgrades are factored into the new James River water quality model. The improvements since 2005 account for some of the 70 percent decrease in projected costs that large polluters face for complying with the new framework, she said.

But controversy continues. Some environmental groups say the new criteria give polluters too much license to exceed their limits. The measure would allow chlorophyll limits to be surpassed by as many as two seasons in six years.

But because the regulation considers springs and summers separately, that could allow up to four failing seasons — two springs and two summers — and still produce a passing grade. If those high chlorophyll seasons happen consecutively, the ecological consequences could be devastating, Brunkow said.

“Our concern is if you allow that back-to-back years of exceedances, you’re not allowing the system to rebalance itself,” he said.

DEQ officials say that exceedances are expected to be small and unlikely to do much harm. The daily and monthly limits will act like a backstop to keep the severity of potential algae blooms in check.

Wastewater industry representatives are pushing the DEQ to take those short-term checks off the table. They question whether a scientific link exists between a single day’s exceedance and a sudden downturn in the river’s health. The short-term limits would force facilities to construct systems to unnecessarily high and expensive standards, they say.

“It doesn’t make sense to build 30-year facilities around one day,” said Chris Pomeroy, general counsel for the Virginia Association for Municipal Wastewater Agencies.

Robertson said the short-term limits are necessary to hedge the agency’s bets against the uncertainty of the model. “We’re trying to ensure protection of aquatic life, so having both sets of criteria working in tandem shores up the protection,” she said.

The James River has been slow to give up its secrets. But those involved in the regulation’s development say the latest effort should help the river recover more fully.

“We’re happy with the outcome,” Brunkow said. “It’s been a long process for sure. For the most part, these are good criteria and we’re excited to move them into the next phase of the process.”