This report summarizes the distribution of phytoplankton biomass, measured as cholorophyll a concentration, and selected hydrographic properties in South San Francisco Bay during 1987.There were 20 cruises during the year, with the most frequent sampling during the spring.The parameters measured were: chlorophyll a, phaeopigments, in-vivo fluorescence, turbidity, Secchi depth, salinity, and temperature.

Water samples were collected in the San Francisco Bay estuary during 42 cruises from February, 1988, through December, 1989.Conductivity, temperature, light attenuation (turbidity), and in-vivo fluorescence were measured longitudinally and vertically in the main channel of the estuary from near the Dumbarton Bridge in the extreme southern part to Rio Vista on the Sacramento River.Discrete water samples were analyzed for chlorophyll a. Water density was calculated from values for salinity, temperature, and pressure (depth), and is included in the data summaries.

Horizontal transects of surface salinity and in-uiuo fluorescence indicate the ex~stence of three d~stinct spatial reglmes in South San Francisco Bay A mid-Bay region of low phytoplankton blomass with little small-scale variance is bounded to the north and south by water masses having higher in-uiuo fluorescence and enhanced small-scale variability. Autocorrelation analyses demon- strate that the length scale of phytoplankton patchiness is longest In the mid-Bay region. The persis- tent discontinuities of in-uioo fluorescence and salinity are associated with topographic features - a large shoal to the north and a constriction to the south. The three spatial reglmes are consistent with measured zooplankton distributions, existing current meter data, estimated longitudinal transports. and numerical simulations of residual circulations that show one (and perhaps rwo) large-scale gyreis) bounded by the northern shoal and southern constriction. Topographic features are the most impor- tant physical factors controlling mesoscale ( - 10 kni) variability of phytoplankton in South San Fran- clsco Bay. We speculate that vertical current shear and salinity stratification (and their effects upon turbulence and diffusion) control small -scale patchmess, but quantitative estimates are needed to determine the influence of large-scale (and local) phytoplankton growth and loss processes