Last year began with a flood and ended with a drought.

The extremes played havoc with water quality, and may have set up conditions that allowed a nuisance species of algae to gain ground in part of the Chesapeake.

River flows into the Bay during the first six months of 1998 were the highest on record, but flows were below average for each of the last six months of the year, according to the U.S. Geological Survey.

December flows were the lowest on record and, while flows rebounded somewhat in January, the new year still started off with drier-than-normal conditions, especially for southern areas of the watershed, according to the USGS.

The high flows early in the year were reflected in the Bay Program’s water quality monitoring, which showed that March through May had some of the lowest dissolved oxygen concentrations seen in the Chesapeake, both in severity and in the amount of water affected.

Oxygen conditions rebounded later as flows were reduced, although dissolved oxygen concentrations remained below average for months. Salinity in huge portions of the Bay were also reduced much of the year.

Strong flows set up ideal conditions for oxygen depletion. They carry large amounts of nutrients into the Bay, fueling algae blooms. When the algae die and sink to the bottom, they decompose in a process that depletes oxygen in bottom areas.

The strong flows also create a barrier that prevents oxygen-rich top layers of the Bay from replenishing oxygen-starved bottom layers.

Meanwhile, some scientists were troubled that increasingly common high flows years may be contributing to a greater abundance of blue-green algae in the Bay. “We look at blue-greens as an indicator of bad water quality,” said Richard Lacouture, a scientist at the Academy of Natural Sciences’ Benedict Estuarine Research Center. “And, it is also a bad food source.”

Typically, blue-green algae are not eaten by larger zooplankton which, in turn, may be eaten by fish and thereby support what is considered to be the desired food web in the Bay. “They’ll spit them out, basically,” Lacouture said. Instead, blue-green algae tend to be consumed by smaller zooplankton, or not at all, in which case, they sink to the bottom and are decomposed by bacteria.

Blue-green algae blooms are common in fresh water, especially in ponds and lakes where large amounts of nutrients fuel blooms in slow-moving water. In the 1970s and 1980s, massive blue-green algae blooms filled the tidal freshwater portions of Potomac River in summer months as flows died down.

Those blooms became a symbol of the Potomac’s pollution problems, but pollution control efforts — particularly those at the District of Columbia’s wastewater treatment plant — nearly eliminated the blooms until the last few years when they have made a comeback, probably because of the large levels of nutrients flushed into the Bay during a series of high-flow springs followed by low-flow summers.

But Lacouture said he has seen an unidentified species of blue-green algae in saltier portions of the Bay, and in gradually increasing abundances, since 1993. Last year, he said, high concentrations stretched from the Bay Bridge to the Potomac River — an area too salty to support freshwater blue-green algae species.

Larry Haas, of the Virginia Institute of Marine Science, noticed what appears to have been the same species during monitoring in the Great Wicomico River, just south of the state line. Because it was a blue-green algae, Haas initially assumed it was coming downstream from fresh water areas. But subsequent monitoring showed that the algae was coming from the Bay.

Haas said that during the 1980s, he studied related algae species in a nearby area of the Bay, but never saw this species. “It just struck me as kind of interesting that it seemed to have recently appeared,” he said.

Harold Marshall, a scientist at Old Dominion University who tracks algae blooms for the state of Virginia, said it was difficult to say whether the species was new to the Bay. While blue-greens are more often associated with fresh water, he said there are also numerous marine species. Because many of the species are small, nondescript and present only at low concentrations, they are not easily identified. But, he said, if it appeared that the species was becoming more abundant, it would be grounds for concern. “Virginia and Maryland laboratories will be paying special attention to this whole category [of blue-green algae] this summer,” Marshall said.

Lacouture said exactly why the species is showing up is hard to explain, although he said it is likely that the spate of recent high-flow years was likely a factor, not only because they increase the amount of nutrients, but also because they could change the ratio of nitrogen and phosphorus that enters the Bay, possibly favoring certain species.

Last year, the USGS said the freshwater flow into the Bay averaged 97,700 cubic feet per second, or 25 percent above average. The average annual flow over the 48 years it has been monitored by the USGS is 78,200 cfs.

The low flows that marked the end of 1998 continued into 1999, according to the USGS.

January flows averaged 80,200 cfs, about 10 percent less than the 88,900 cfs average for the month. But the source of the flows changed dramatically: 58 percent came from the Susquehanna, which normally provides about half the freshwater entering the Bay, while only 14 percent came from the Potomac, which normally supplies a quarter of the Chesapeake’s fresh water.

That is roughly in line with a long-term prediction issued by the National Weather Service last fall. As a result of influences from La Nina, a relative of El Nino which was blamed for much of the above-normal rainfall last winter, the weather service predicted a slightly wetter than normal winter for upper portions of the Bay watershed, with drier-than-normal conditions for lower portions of the basin.