A surge of storm water and pollution from Pennsylvania and New York was flowing into the Chesapeake Bay through the Conowingo Dam again last week, raising concerns that the relentlessly rainy summer could threaten oyster reproduction and throw off bay ecology for some time.

Even as scientists were assessing the environmental impact from recent storms, rising Susquehanna River waters were prompting dam operator Exelon Corp. to open Conowingo floodgates for the second time in three weeks, sending a deluge of muddy brown water into the upper Chesapeake.

“The water right now really looks like chocolate milk,” said Cindy Palinkas, an associate professor at the University of Maryland Center for Environmental Science. “I’ve never seen that before.”

Palinkas led a research trip last week to a large bed of grasses at the mouth of the Susquehanna. Scientists were already concerned about the impact the record July rainfall could have on oysters, which need salty water to reproduce successfully. And they still have questions about the long-term effects of an influx of nutrient pollution and plastics that the floodwaters carried.

Now, the bay is facing another round of stress.

“It’s the event that doesn’t go away. It keeps unfolding,” said Doug Myers, Maryland senior scientist for the Chesapeake Bay Foundation.

Exelon officials expected to open 10 to 13 of the Conowingo’s 52 gates Thursday, about half as many as they opened during late July flooding.

The company has been the target of criticism from Gov. Larry Hogan, whose administration has demanded that it do more to prevent pollution from getting past the dam. Exelon responded by suing the state, saying it should not be held responsible for pollution it doesn’t create.

Hogan said that he recently had “a pretty direct discussion with the chairman of Exelon” and that he plans to continue to press the company to help in Chesapeake cleanup efforts. He said the state will meanwhile solicit proposals within the next month for a test project to dredge sediment and nutrients that have built up behind the dam.

The nonstop rain and flooding are only making the problem worse, said Mark Belton, Hogan’s secretary of natural resources.

“We have been watching very closely the flow of the Conowingo Dam . . . to understand the nutrients that are coming over and to understand what type of debris might be coming over,” he said. “That’s really gunked up the bay.”

It could still be weeks or months before the repercussions of all the storms become clear in the Chesapeake. Scientists worry that large amounts of nitrogen and phosphorus washed into waterways could fuel algae blooms that could eventually strip portions of the bay of oxygen. Large amounts of sediment could smother plants and shellfish and block sunlight.

But they aren’t seeing their worst fears yet — in fact, for now, the rains have cleared the bay of a lot of algae, Myers said.

“The entire bay has been flushed of some of the normal harmful algae species that might bloom in the summertime,” he said.

That surge of fresh water is not good for all creatures in the bay, though. Oysters need warm, salty water to spawn larvae that end up attaching to reefs, becoming what are known as spat. But all the rain has prevented ocean water from making its way into the middle and upper portions of the bay.

Myers said bay foundation scientists aren’t seeing signs of the next generation of oysters anywhere in the middle and upper portions of the bay. Water near Annapolis is almost fresh enough to drink, he joked, but if it doesn’t become saltier before fall, that could be devastating for oysters.

“If it gets cool before it gets salty again, then they may not reproduce this year,” he said.

In the northernmost reaches of the Chesapeake, if waters stay too fresh for too long, it could kill some adult oysters, said Michael Roman, director of the University of Maryland center’s Horn Point Laboratory. But the species is resilient.

“They’re adapted to these conditions,” Roman said. “It is rare to have this much fresh water coming in in July like we’ve had, but I’m sure it’s happened before.”

On the other hand, diseases that plague bay oysters also like salty water, he said. So the fresh water could prevent some oyster deaths that might have occurred in more typical conditions.

As another pulse of cloudy water washed onto a bed of underwater grasses in the Susquehanna last week, Palinkas and her colleagues were looking closely to see how the vegetation fared during the last round of sediment-carrying floodwater. They found that even smaller patches of grasses survived, although there were signs of stress on the area known as Susquehanna flats.

Bruce Michael, director of resource assessment service for the Maryland Department of Natural Resources, said it does not appear that the July rain scoured away the buildup of sediment behind the Conowingo that the state plans to explore dredging. The department planned to perform regular sampling of water quality and habitat conditions this week to assess the impact of this week’s surge of Susquehanna water.

The river clearly carried significant amounts of sediment from other dams upriver, and from across central Pennsylvania and western New York, though.

The riverbed appeared muddy and black last week, Palinkas said. Researchers collected samples of the sediment and of the grasses to measure the nitrogen and phosphorus they contain.

They hope to find that the grass beds are fulfilling an important ecological function, trapping the contaminants before they can fertilize algae blooms downstream in the bay.

There are signs that they did just that during the July flooding, although it will be a couple of months before the scientists know for sure. Satellite images of the bay after July flooding show a plume of mud and debris flowing down the Chesapeake, but also a bright green spot at the mouth of the Susquehanna — the flats.

“That’s a very strong suggestion they’re trapping a lot of sediment,” Palinkas said. “They’ve been resilient so far.”

— Baltimore Sun