In large lake systems the nearshore habitat is an intermediate zone between the shoreline and offshore, is an important nursery for larval fish, and is highlighted as an area in need of research in the Laurentian Great Lakes. In this study, we used two long-term monitoring programs to characterize the nearshore zooplankton community composition using seasonal data (May – October) and to compare the nearshore and offshore zooplankton community composition changes over time (1998 – 2019) to determine if the changes were synchronized. In the nearshore, we found the highest zooplankton biomass during the late summer/early fall (August 27th – Oct 6th), compared to mid-summer (July 1st – Aug 26th) and late spring (May 20th – June 30th). In the summer, the nearshore zooplankton community was dominated by cladocerans while copepods dominated the offshore community. From 1998 to 2019, both nearshore and offshore copepods shifted from a cyclopoid to a calanoid-dominated state, but the details of this change were different. For example, taxon-specific analysis revealed that despite reduced cyclopoids in both habitats, Mesocyclops edax increased in the nearshore. Additionally, taxon-specific analysis suggested the changes occurred an average of three years earlier in the nearshore. Using Analysis of Similarity, the nearshore and offshore summer zooplankton community compositions became increasingly distinct over time. Results from this study highlight the uniqueness of the nearshore in large lake systems, the importance of seasonal and long-term monitoring, and the potential of the nearshore as an early indicator of offshore changes.