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Temperate estuaries are characterized by significant seasonal variability in the vertical salinity gradient, which, along with biological factors, may play a role in determining plankton ver- tical distribution. We examined the vertical distribution of microplankton (20 to 200 µm) and nanoplankton (~5 to 20 µm) in the San Francisco Estuary (SFE) over diel, seasonal and interannual time scales, and assessed the degree to which abiotic (hydrography) and biotic (predation) factors influenced these patterns. We sampled 2 hydrographically-distinct locations within the SFE: San Pablo Bay, a partially-mixed estuary, and South Bay, a lagoonal estuary. We conducted replicate Niskin bottle casts during the day and night at each location on 6 occasions between 1998 and 1999. We also conducted replicate day and night pump sampling for mesozooplankton (>153 µm) on 4 of these dates. The vertical distribution of micro- and nanoplankton was often homogeneous with depth, even under substantially different hydrographic conditions. ANOVA testing of weighted mean depths (WMD) of chlorophyll, major taxa of micro- and nanoplankton, and cope- pods (factors: location, year, season, time of day) revealed that only the microplankton taxa (specifi- cally ciliates) showed significant differences in vertical distribution over the sampling period. The most significant differences in WMD were observed seasonally. Ciliates and copepods (Acartia spp.) showed significant diel differences in WMD on several occasions, but diel differences were rarely observed among other micro- and nanoplankton. The degree of salinity stratification was never correlated to WMD of any micro- or nanoplankton group, however vertical distributions of heterotrophic loricate and aloricate ciliates and dinoflagellates were often significantly correlated with distributions of chlorophyll and autotrophic nanoflagellates (presumed food), as well as with the vertical distributions of Acartia spp (presumed predators). We conclude that micro- and nanoplankton are often relatively homogeneously distributed with respect to depth in the SFE. However, when micro- and nanoplankton distributions were more heterogeneous, biotic factors had a greater influence on vertical distribution than abiotic factors (stratification) in the SFE.

Vertical distribution of micro- and nanoplankton in the San Francisco Estuary in relation to hydrography and predators