Scientists who expected this year's dry conditions to produce clear Bay waters were surprised as much of the Bay and its tidal tributaries were instead choked with algae blooms this summer.

From fish-killing blooms in the Potomac River and Baltimore Harbor to a mid-August bloom that coated the Elizabeth and Lafayette rivers, various species of algae have stained the region's tidal creeks, rivers and embayments with hues of red, brown and green while contributing to low-oxygen levels.

Poor water clarity is often associated with high river flow years, when pounding rains flush huge amounts of nutrients into tidal waters, where they fuel algae growth. Along with the nutrients are plumes of sediment, which cloud the water.

"You would think that you would see better water clarity because you have less runoff," said Bruce Michael, who heads the Maryland Department of Natural Resources tidal monitoring program. "This year that really hasn't been the case. Our water clarity has been considerably worse than it has been in past years."

Michael said it's possible that spring rains brought enough nutrients to fuel the blooms in the tributaries, but not a strong enough flow to flush the blooms farther downstream where they would be diluted.

Another contributing factor, he said, is the low flows washed less sediment into the rivers. With less sediment clouding the water, more light was available to spur the growth of algae, which make use of the available nutrients.

Flows into the Bay were below average in May through July. According to the U.S. Geological Survey, July flows into the Bay were 18,900 cubic feet per second, half of the average for the month. Flows were also lower than normal in the early winter.

Dry conditions in 2002, in contrast, brought record water clarity that resulted in a huge comeback in underwater grasses. This year, biologists worry that widespread blooms could cause losses of grass beds.

A key difference, said Rich Batiuk, associate director for science with the EPA's Bay Program Office, is that conditions had been dry for more than a year prior to the summer of 2002, meaning less nutrients were washed into the Bay that spring.

This year, river flows into the Chesapeake were near normal for a short portion of late winter and early spring, which may have pushed enough nutrients into the Bay and tidal rivers to fuel the blooms, he said.

"That, with a little bit of thunderstorm activity, will give us enough nutrients for them to pop up," he said. "That is what I think we are seeing this summer, so far."

The bottom line, he said, is that the Bay is too overwhelmed with nitrogen, phosphorus and sediment.

Of great concern this year is that many blooms have been caused by Karlodinium, a type of algae that can produce toxins. While the dinoflagellate has always been present, this year it produced more-and denser-blooms than seen before.

"It's been an outrageous year," said Allen Place, a biochemistry professor at the University of Maryland Biotechnology Institute's Center of Marine Biotechnology, who has studied Karlodinium extensively.

Karlodinium produces a toxin to paralyze the small algae it feeds upon. When it forms dense reddish-brown blooms, the toxin also reaches concentrations lethal to fish, although it has not been shown to harm humans. Karlodinium can kill fish at concentrations as low as 10,000 per milliliter. In one bloom this year, Place said, he measured cell concentrations of 900,000 per milliliter.

A bloom, largely of Karlodinium, began June 11 on the Potomac River and lasted for more than a month, at times covering more than 30 miles, from upstream of Colonial Beach to Sandy Point downstream.

In mid-July, a major fish kill took place in a Potomac tributary, Maddox Creek, just below Colonial Beach, involving more than 300,000 fish. About 56 percent were menhaden, 30 percent were white perch and 12 percent were croaker. Gizzard shad, mummichog, blue crabs, American eel and other species were also among the dead. Karlodinium cell counts were as high as 70,000 per milliliter. Dissolved oxygen was often at levels considered stressful to fish.

In addition, Place said, Karlodinium was found in association with at least 10 fish kills in Maryland through mid-August, although it was unclear whether it was responsible for all of the kills.

He said Karlodinium was probably proliferating because it prefers salinities around 9-10 parts per thousand. This year's low flows allowed it to move upstream, where it encountered blooms of other algae, giving it plenty to feed upon.

"Our current belief is that 'Karlo' could never bloom unless it was eating," Place said. "It just doesn't have a high enough division rate when it is acting like a plant (by living off sunlight). But when it is eating like an animal, its division rate is nearly four times faster."

Not all blooms-or even all lethal ones-were caused by Karlodinium. In late May and early June, a large bloom of Prorocentrum minimum in Baltimore Harbor led to a kill of about 7,000 fish, mostly menhaden, when cells began dying and using up oxygen in the water.

It was replaced with blooms of Karlo-dinium and other species which discolored the harbor for most of the summer.

Scientists expected blooms to continue until fall, when changes in temperature and winds typically end outbreaks.

In mid-August, a large mahogany bloom of Cochlodinium polykrikoides, a dinoflagellate, spread across parts of the Elizabeth River and nearby areas. Harold Marshall, a phytoplankton expert at Old Dominion University, said he expected the algae to make its way into other rivers. "We anticipate this species to be a common bloom producer occurring in many of the tributaries along the western shoreline of the Chesapeake Bay this summer and into early fall."

The Bay and its tidal tributaries are home to about 1,400 species of phytoplankton, many of which are capable to forming blooms if they encounter the right conditions. This year shows that when environmental conditions change, there will be a species around to take advantage of the situation, Marshall said.

"Even if it is a dry year, there are many of these species that will find the conditions favorable for development, and even bloom development," Marshall said.

This year's barrage of blooms also illustrates the rationale for the water quality criteria for chlorophyll a. Most of the Bay region's nutrient and sediment reduction goals are aimed at achieving water quality standards that set minimum acceptable levels of dissolved oxygen and water clarity in various parts of the Bay. They are aimed at protecting aquatic life a well as the survival of underwater grass beds.

But the Bay states have also adopted some standards for chlorophyll a-a measure of algae in the water-and more are in the works. The standards are aimed at preventing chlorophyll concentrations associated with harmful algal blooms.

Batiuk said that even when Baywide nutrient and sediment goals are achieved, it's possible that some slow-moving tidal creeks and embayments would still accumulate harmful levels of algae unless they are specifically targeted for nutrient reduction efforts.

He said this year's blooms may provide clues about possible problem areas where extra efforts may be needed to meet chlorophyll a standards, and thereby limit harmful algae blooms in the future.

"The criteria address a specific set of water quality impairments that might be partially, but not fully, addressed with our focus on dissolved oxygen in the mainstem Bay and water clarity in the shallows," Batiuk said. "'Bay cleanup' also means these shallow waters, and these small embayments."