Three related data sets from a baseline environmental survey on the continental shelf at San Onofre, California, consisting of: (1) zooplankton pumped from discrete depths on transects between the 8- and 30-m contours, sampled from 1976 to 1980; (2) zooplankton from oblique net hauls on a transect from 8 to 100 m sampled at 2-week intervals for 1 y, 1978–1979; and (3) vertical profiles of temperature, nutrients and plant pigments corresponding closely in time and space to the oblique net hauls, are used to describe cross-shelf zooplankton abundance patterns, community composition, and seasonal and shorter-term variations in cross-shelf zonation and their relation to variations in physical and chemical measures. Of 15 taxa tested for multiyear average patterns, three—the copepods Acartia clausi and Oithona oculata, and barnacle larvae—had centers of abundance shoreward of the 30-m contour and near the bottom. No differences were detected in the cross-shelf pattern between San Onofre and a transect 12 km southeast. Throughout the year, nearshore and offshore assemblages were distinguishable, the change occurring at about the 30-m contour. The offshore one, represented by the copepods Calanus pacificus, Eucalanus californicus and Rhincalanus nasutus, occupied water having less chlorophyll and less near-surface nutrient, i.e. of more oceanic character. In spring and summer, most nearshore taxa shifted slightly seaward, leaving a third assemblage, characterized by a very high abundance of Acartia spp. copepodids and maximum abundances of A. clausi and O. oculata near the beach. Three upwelling episodes resulted in marked increases in chlorophyll and nutrients, but not in cross-shelf gradients of these properties, as were noted at most other times. Maximum disturbance of cross-shelf zooplankton zonation was observed during a wintertime intrusion of offshore surface water, but the zonation was never obliterated. Nearshore zooplankton patterns appear to be protected from dislocation by the shallow shelf and sustained by phytoplankton distributed in a manner peculiar to the nearshore zone. Typically, shallow nearshore waters were richer in chlorophyll and nutrients than offshore waters of the same depth. The cross-shelf chlorophyll and nutrient profiles, in turn, appear to result from increased eddy diffusion and nutrient recycling in shallow waters, perhaps augmented by longshore transport from quasi-permanent, local upwelling nodes.