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ABSTRACT: Diatoms were the dominant phytoplankters throughout the Sacramento-San Joaquin Delta into San Pablo Bay during 1969 through 1977. Green algae seldom exceeded 20% of the total. Chlorophyll a concentrations seldom exceeded 6 µg·liter-1 at the most upstream station in the Sacramento River, the major water source to the Delta, except during the 1977 drought when 40 µg·liter-1 was measured. Conversely, peak summer chlorophyll concentrations entering the Delta from the San Joaquin River were the highest (100-350 µg·liter-1 and were inversely related to riverflow. During spring through fall, export pumping from the southern Delta caused a net flow reversal in the lower San Joaquin River, drawing Sacramento River water across the central Delta to the export pumps. The relatively deep channels and short water residence time apparently resulted in the chlorophyll concentrations remaining low from the northern Delta and in the cross-Delta flow to the pumps. Chlorophyll concentrations in the shallower eastern Delta sloughs and channels were often quite high and variable. Western Delta spring blooms reached concentrations of 25-50 µg·liter-1. Spring blooms of 30-40 and summer blooms of 40-100 µg·liter-1 were observed in Suisun Bay. The entrapment zone location adjacent to the shallows of Suisun and Honker bays appears to increase the Suisun Bay phytoplankton standing crop. Chlorophyll a concentrations in Suisun Marsh generally peaked to 40-100 µg·liter-1 in the late spring except during 1977. Chlorophyll levels in central San Pablo Bay seldom exceeded 6 µg·liter-1, although blooms as high as 40 µg·liter-1 were observed in the northern shallow portion of the Bay. Percent chlorophyll a (of the total chlorophyll a plus the pheo-pigments) in near-surface water generally varied from 50-80% during the spring-fall months throughout most of the study area. Upstream of the entrapment zone, percent chlorophyll a near the bottom averaged about 5% lower than that near the surface. Downstream of the entrapment zone, percent chlorophyll a was as much as 40% lower near the bottom.
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