Ongoing monitoring programs and historical data are not sufficient to establish anthropogenic effects on the water quality and ecology of Chesapeake Bay. However, stratigraphic records preserved in the sediments of the mesohaline Chesapeake Bay were used to reconstruct a 2,000 year history of sedimentation, eutrophication, anoxia and diatom community structure from pre- Columbian to modern times. Diatoms, pollen, total and organic carbon (TOC), total and organic nitrogen, total sulfur, acid-soluble iron, an estimate of the degree of pyritization of iron (DOP), and biogenic silica (BSi) were used as paleoecological indicators in four sediment cores collected in a transect across the Chesapeake Bay from the Choptank River to Plum Point, Maryland. Surface salinities in this area of the Bay average 8-15%.

The four gravity cores (114-160 cm long) were collected in areas that currently experience different patterns of hypoxic and anoxic bottom waters. The sediments within the cores were dated using radiocarbon and pollen techniques. The 14C-determined dates at the bottom of the cores range from 910-2650 years before present. Sedimentation rates were determined (0.2-5.8 mm yr^-1) using pollen methods, and a chronology for each core was compiled. Geochemical indicators were measured and diatom species identified and counted at subsampled 2 cm intervals within each core. More than 400 diatom species, primarily marine and estuarine taxa, were identified in the sediments of the Chesapeake Bay, some for the first time. The taxonomy, autecology, and observed valve morphology of the 50 most abundant species are discussed.

Analysis of the data indicates that sedimentation rates, eutrophication, turbidity, and anoxia have increased in the
mesohaline Chesapeake Bay since the time of European settlement of the watershed and land clearance for agriculture. There is also evidence that freshwater input to this area of the Bay has increased. Changes in diatom community structure and geochemical indicators reflect major changes in land use patterns of the watershed. Large increases in organic carbon and nitrogen seen in the sediment samples, as a function of time, cannot be readily modeled using accepted decay models for reduction in marine sediments. Several DOP measurements dated post-1900 indicate restricted bottom water oxygen conditions in this area of the Chesapeake Bay. Diatom community diversity exhibits a continuing decline since about 1760 A.D., while centric/pennate ratios rise dramatically in most recent sediments. Diatom communities from samples of all four cores dated within similar time periods of land use are shown to be clustered together by the unweighted pair group method using arithmetic averages (UPGMA) of Euclidean distance measures between samples.