The far north of Ontario, Canada, is a region that is very vulnerable to future change due to climate warming and resource extraction. Despite its vast size (~ 450,000 km2) and large numbers of lakes (> 700,000), there has been very little study of aquatic ecosystems in this remote area. To address this lack of limnological data, forty-one northern Ontario lakes spanning two physiographic regions, the Hudson Bay Lowlands and the Canadian Shield, were sampled during 2012 for crustacean zooplankton and water chemistry. These sub-Arctic lakes support diverse crustacean plankton communities with species richness similar to the richness of lakes in central and northeastern Ontario. While some of the species collected appear to be at the northern limit of their distributions, most relatively common Ontario species occurred throughout the 2012 study area. The physico-chemical characteristics showing relationships with species richness and relative abundances were variables associated with lake morphometry, ionic strength and nutrient status. There were differences in community richness and composition between Lowlands and Shield lakes; however, these differences do not seem attributable to biogeographical influences on species occurrences. Rather, the lower species richness and differences in community composition in Lowlands lakes relative to Shield lakes appear to be largely related to lake morphometry. The shallower and generally smaller Lowlands lakes provide much less habitat diversity, i.e. niche space, than the larger, deeper Shield lakes, leading to simpler communities.