This study addresses the regional variation of zooplankton in the Great South Channel area in the southern Gulf of Maine between Cape Cod, Massachusetts and Georges Bank. This is a region of particular interest because of the intense concentrations of the copepod Calanus finmarchicus in the spring, along with the co-occurrence of right whales that feed upon these copepod aggregations. Zooplankton in the Great South Channel were sampled with the MOCNESS plankton sampler during spring 1988 and 1989 as part of the SCOPEX (South Channel Ocean Productivity Experiment) project. Zooplankton variation was addressed through comparisons of taxonomic composition and water column abundances among tows within and between years, and between locations with and without right whales. Results showed that zooplankton community composition was highly similar between tows within each year average percent similarity index (PSI) for pairwise comparisons of tows = 82.2 and 88.8% in 1988 and 1989, respectively] as well as between years (mean PSI = 84.4). The copepods C.finmarchicus and Pseudocalanus spp. dominated the zooplankton in terms of total water column abundance (>94% of all zooplankton), with C.finmarchicus comprising an average of 84% of the copepods. Highest abundances of these copepods (particularly the younger life stages) coincided with a region of low-salinity transport from the north. In addition, these copepods had higher abundances in 1989, which may be related to the fact that low-salinity transport was approximately twice as large in 1989 as in 1988. Given the physical dynamics of the region, it is possible that developing copepod populations were adverted into the Great South Channel from the northwestern Gulf of Maine via the low-salinity plume. Each year, whales were located in areas of both high and low copepod abundance, and tended to concentrate near the leading edge of the low-salinity plume. In 1988, there were no significant differences in zooplankton abundance between right whale areas and non-whale areas for any taxon. In 1989, whale areas had a greater proportion of C.finmarchicus relative to other zooplankton in 1989, which suggests that whales preferred regions enriched in C.finmarchicus.