Samples from 146 lakes in the northeastern United States, collected during Phase II of the Eastern Lake Survey (ELS-II) were analyzed for abundance of each species and each size class of zooplankton. The composition of zooplankton assemblages (not abundance) exhibited clear relationships with physical and chemical features of the lakes. Assemblage structure was examined at various levels: diversity, major genera, and individual species. Genera and species level identifications revealed the clearest relationships to water chemistry, although significant relational patterns were discerned using only major taxonomic groups or size structure information. Significant regional influences (biogeographic patterns) were also observed at various levels of organization (major taxonomic groups, genera, species, and diversity). These results illustrate the utility of studying zooplankton assemblages as sensitive indicators of water chemistry. The report makes recommendations for improving methods of relating zooplankton species to environmental factors.