The menu for some tiny animals in the Patuxent River may be undergoing dramatic changes. Once, tiny crustaceans known as copepods used to dine on a particular type of algae in the river.

But experiments using giant tanks of water from the river, known as mesocosms, indicate that their favorite algae is being wiped out by relatively low amounts of arsenic in the water.

In its place is a smaller but more arsenic-resistant species.

The problem for the copepods is that they either don’t like — or can’t eat — the new, smaller algae. “Basically, they like their food in particular sizes and shapes,” explained Jim Sanders, a researcher at the Academy of Natural Sciences’ Estuarine Research Center.

That may explain why they, too, are in sharp decline in the mesocosms, which are designed to reproduce actual river conditions in a way that is easier to study.

If what happens in these studies is taking place in the river, it would be worth noting because many things — such as some fish — depend upon copepods for a major portion of their diet.

Does that mean low levels of arsenic result in fewer fish?

No one knows.

But it illustrates why scientists are having a hard time answering one of the most perplexing questions about the Chesapeake: Does it have a toxics problem?

A new report summarizing recent toxics research in the Bay indicates that while scientists have started to understand many of the complexities that affect chemical contamination in the Chesapeake, it’s unclear whether the Bay has a “problem” with toxics outside three well-known “hot spots” where fish have exhibited lesions and cancers: portions of the Elizabeth and Anacostia rivers and Baltimore Harbor.

The report, “Chemical Contamination in the Chesapeake Bay,” was produced by the Sea Grant College Programs of Maryland and Virginia. It summarizes a workshop held by scientists and water quality managers which reviewed the state-of-the-knowledge after five years of focused research in the Bay. The report, and some of the workshop participants, point out that there is no obvious Baywide contamination problem leading to highly visible impacts such as fish kills or cancers. At the same time, the report raises warning flags about the impacts that low levels of contaminants may have in many regions of the Bay.

“There’s no smoking gun,” said Bess Gillelan, director of the National Oceanic and Atmospheric Administration’s Chesapeake Bay Office, which has funded most of the research that went into the report. “But there are lots of things that you wouldn’t notice unless you’re looking in the right way. And I think that is going to be the challenge for us — to figure out how we can devise a research strategy for the next five years so that we can look for some of those subtle effects.”

Besides the changing algae population in the Patuxent, for example, the report notes that oysters exposed to chemical contaminants have been shown to be more vulnerable to disease. Chemical preservatives such as those used in wooden bulkheads result in the loss of species in nearby areas. Some evidence suggests that contaminants running off farmland, suburban developments or city streets into areas thought to be “clean” may cause toxic impacts, such as killing fish larvae, in certain situations.

All of this indicates that defining the “problem” is, itself, a problem. Historically, chemicals have been controlled based on their ability to kill fish or pose a threat to humans who eat the contaminated fish. Less clear are whether “sublethal” effects, such as changes in algae populations which may ripple through the food chain, or reduced reproduction, are a “problem.”

“That’s an argument not only among the managers, it’s an argument among scientists,” Sanders said. “I don’t think anybody would argue that when you have a significant amount of a fish population with cancers, you’ve got a problem. The arguments occur as to whether or not some of the less obvious, more insidious things are equally important.”

In the late 1980s, NOAA’s Chesapeake Bay Environmental Effects Committee funded research about the Bay’s problem with anoxia — the lack of oxygen in certain areas during the summer.

After five years of work, a report was issued linking anoxia — considered to be the Bay’s primary water quality problem — to an excess amount of nutrients entering the Chesapeake and other factors.

With that issue addressed, the committee turned its research to toxics. But after five years, the issue remains murky.

The reason for the difference is that anoxia was largely the impact that excessive amounts of two nutrients — nitrogen and phosphorus — had on the Bay. They triggered algae blooms that depleted the water of oxygen when they died, sank to the bottom and decomposed.

By contrast, more than 1,000 chemicals have been found in the Bay.

Not only are there more substances than nutrients, but many factors determine whether a particular contaminant poses a toxic threat. Much of the research in recent years has focused on understanding those factors. For example, the amount of the contaminant in the water is critical to its toxicity, but a range of natural conditions such as the salinity and acidity of water can also affect whether a particular chemical impacts an organism.

The presence or absence of oxygen at the bottom is also critical: When oxygen is depleted, some contaminants are trapped in the sediments, while others are released into the water column where they are exposed to fish and other creatures.

Different “species” of the same chemical have different effects. For example, the report notes, the form of copper used in antifouling paints is highly toxic to many living organisms, while other forms of copper may be less toxic.

Chemicals can mix together in the water, causing unknown effects. And some contaminants rapidly break down into less harmful substances, while others — particularly many old, banned chemicals such as DDT or PCBs — can remain intact for years.

But even the presence of such contaminants doesn’t mean a problem exists. For example, the Bay generally has higher concentrations of PCBs in the water than the Great Lakes, noted Joel Baker, a researcher at the University of Maryland’s Chesapeake Biological Laboratory, who has worked in both places. Yet PCB concentrations in Great Lakes fish are high enough to warrant widespread fishing advisories, while PCB contamination has not been shown to be a problem in Chesapeake fish.

“It doesn’t seem as though estuarine organisms accumulate chemicals to the same extent that the lake organisms do,” Baker said. “And whether this is due to migration patterns, or some basic difference in their feeding physiology, or we just don’t have enough data, I don’t know.”

Human activities not related to contaminant discharges can affect their distribution in the Bay.

For example, algae blooms caused by excess nutrients can absorb contaminants at one location — which otherwise would settle to the bottom — and transport them someplace else. When the algae sink, they may expose bottom dwelling benthic organisms in otherwise “clean” areas to contaminants.

And as the algae die and decompose, they deplete the water of oxygen, which in turn traps some contaminants at the bottom, while releasing others into the water column.

“Every little change we make has a ripple effect,” said Bill Rickards, head of the Virginia Sea Grant College Program. “Every time we impact the system in any little way, there’s a ripple that goes over to other animals or plants.”

Whether toxics “go away” by being buried in the sediment depends on what part of the Bay they are located in. Currents, waves, dredging activity — even burrowing worms — can stir chemicals that have settled on the bottom back into the water. And if one of those borrowing worms is eaten by something else, the chemical can move directly into the food web.

Despite the great complexities, scientists have gradually been piecing together a picture of the Bay indicating what issues and processes are most likely to affect contaminants in different parts of the Bay: How they move through an area; where contaminants are most likely to be “trapped” in sediments and where chemicals that settle to the bottom are more likely to be put back into the water column; and what happens to different types of contaminants — such as heavy metals, or PCBs — in different areas.

But taking the next step — determining whether those contaminants are posing significant threats to organisms living in different parts of the Bay — still looms as a major question.

“I think we’ve made quite a lot of headway as a regional group of scientists in the last five years,” Sanders said. “The hard thing to get a handle on is what level of biological effect we need to worry about, and can we regulate any of these to reduce those impacts. And I think we’re still five to 10 years away from making a significant dent in that question.”

The Patuxent River algae illustrates the point.

Algae are known as “primary producers” — tiny plants that convert sunlight into energy — which form the base of the Bay’s food web. They are eaten by zooplankton (tiny animal organisms) such as copepods. Some are eaten by small fish. They, in turn, are eaten by larger and larger fish, or by humans, animals or birds.

So a wholesale change in the algae population, which also affects the species that feed on them, could have the potential to disrupt the entire food web. But whether that happens is unclear.

Estuaries such as the Chesapeake Bay are tremendously productive areas. Some modeling and laboratory work indicates that changes at the bottom of the food web are not always felt at higher levels because there is — in effect — more than enough to go around.

“Ecosystems are pretty flexible,” Sanders said, “and there are species that tend to take over for one another. It may well be that ecologically, the system doesn’t get affected much when you see a low-level change like that. But that doesn’t mean it won’t.”

Indeed, the report noted that other research shows that such changes can have ripple effects. For example, a study done in the Great South Bay of Long Island during the 1950s found that a shift in phytoplankton size toward smaller cells because of excess nutrients resulted in a decline in the oyster population because the smaller algae was no longer suitable food.

Finding and understanding the implications of such shifts is difficult work, scientists say.

And, it is made even tougher because the sources of contamination are becoming more complex.

Contrary to the popular view, the report notes that most contaminants originate not from industries — which have reduced emissions as a result of the Clean Water and Clean Air acts — but from stormwater runoff, auto exhaust, household chemicals such as pesticides and solvents, and other diffuse sources that wash into the Chesapeake and its tributaries.

“The public, by in large, has a misperception about the Bay,” said Chris D’Elia, director of the Maryland Sea Grant College. “The general perception is that the Bay has been degraded because greedy industries release lots of toxic materials into the Bay which are killing things, and that is why the Bay’s bounty isn’t as good as it used to be. That may have once been true, but there has been major progress in controlling industrial inputs in the last several decades. Concern now rests with the individual citizen. What you and I do — in effect, how we change our behaviors — will be the key in the future.”

Assessing the impact of contaminants from a wide variety of sources that may periodically be flushed into the Bay after rainfalls, and at greatly varying concentrations, adds another degree of complexity.

“It’s hard to say what the organisms think about getting hit with a chemical load every once in a while,” Baker said, noting that most laboratory studies and computer models assume that organisms are exposed to a steady flow of contaminants.

Yet evidence suggests that may be a concern. One project funded by the Bay Program found “spikes” of contaminants in areas of the Eastern Shore where there are no industrial sources.

The same project exposed a variety of species to water sampled from nine sites around the Bay and found toxic effects at most of the test stations. The following year, few effects were observed, an indication that impacts may vary with the runoff from year to year.

A better understanding of contaminant issues may be critical not only for organisms, but for decision makers. In a system as complex as the Bay, organisms are affected not only by contaminants or nutrients, but by a range of environmental stresses.

If nutrients — and therefore the amount of algae — are reduced in the Bay without also reducing the amount of contaminants, the report notes, the remaining algae may actually face increased, rather than decreased, contaminant exposure in parts of the estuary.

“We haven’t really thought too much about the interplay between the two,” Baker said. “Estuaries are complicated.”

He said that studies in the Baltic Sea have shown chemical concentrations in fish have increased as nutrient levels decreased. There are hints that the same thing has happened in the Great Lakes, Baker said. “Basically, there are fewer fish and they grow more slowly because there are less nutrients and they get fatter and older,” he said. “Fat and old relate to higher levels of chemical contamination.”

Baker said that doesn’t mean that nutrients should not be reduced, but that more research is needed on the issue.

And, Sanders said, without a better understanding of all the stresses facing fish and other Bay species, the Chesapeake may not recover as fully as possible.

“I still believe that the most important issue we have is nutrients,” he said. “That is the one issue that absolutely has to be dealt with, and I think we will reach a level of recovery because of what is going on right now. Everyone is assuming that the more you turn down those nutrient loadings, the more the system will recover to the way it used to be. However, I think that underlying that are contaminant issues that we don’t understand very well. And if we don’t get at them, we may find that the Bay comes back only part way, and there may be something else that is keeping it from coming back the rest of the way.”

For a copy of the Sea Grant report, “Chemical Contamination in the Chesapeake Bay: A Synthesis of Research to Date and Future Research Directions,” contact the Maryland Sea Grant College, by phone, (301) 405-6376, or fax (301) 314-9581.