<em>Abstract.</em>—Pacific herring <em>Clupea pallasi </em>is a commercially and ecologically important fish with a sizable stock that spawns and spends its early life history in the San Francisco Estuary (SFE). Yet very little is known about the basic ecology of larval Pacific herring in the SFE. We undertook a 3-year field study (1999–2002), focused on winter and spring collections in two regions of the SFE (the Central and San Pablo bays), to address three objectives: (1) determine seasonal abundance patterns of larval Pacific herring in the two bays, (2) examine the diet of larval Pacific herring, and (3) evaluate the condition of larval Pacific herring in the two bays. Pacific herring were a conspicuous component of the winter larval fish assemblage in both the San Pablo and Central bays, comprising a maximum of 22.5% and 5.5% of total abundance, respectively. Larval Pacific herring abundance peaked in February or March of each year, reaching a maximum density of 2.53/m<sup>3 </sup>(San Pablo) and 0.52/m<sup>3 </sup>(Central Bay). Length frequency distributions suggested that at least 2–3 cohorts were produced each year, with some evidence that larvae were slightly larger in San Pablo Bay. Larval Pacific herring fed on a broad range of prey types, including tintinnids, copepodids, copepod nauplii, diatoms, and gastropod veligers. The unusually high proportion of tintinnids in the diet (87% by number in March 2001) suggests an important protozoan–metazoan linkage. Condition of larvae was assessed by analyses of covariance of a “growth sensitive” variable (i.e., body weight, anal body depth, or pectoral body depth) regressed against a “growth insensitive” variable (i.e., standard length). These results showed marked differences between the bays: in Central Bay, early (small) larvae exhibited better condition, but within San Pablo Bay, larvae exhibited a greater rate of improved condition with increasing age (size). This suggests the possibility of important differences in the Central and San Pablo bays as larval Pacific herring nursery grounds. Several areas of future research on the ecology of larval Pacific herring in SFE are recommended (e.g., coupling between horizontal and vertical distributions and advective flow fields, predation, and feeding dynamics on protozoan versus metazoan prey).
