Zooplankton are the major conduit of energy from phytoplankton to planktivorous fish in the freshwater pelagic zone and influence two common management goals including reducing phytoplankton populations by grazing on them and maintaining fisheries as food for planktivorous fishes. Zooplankton are commonly suggested as ecosystem indicators because they are short lived and respond quickly to ecosystem changes. Additionally, their community composition may indicate ecosystem condition due to their diverse life histories and feeding guilds. Zooplankton are also relatively cheap and easy to collect, compared to intensive fishery surveys, and their use can be tested locally in systems with existing data. In this dissertation, I used long-term zooplankton community composition data to better understand the Great Lakes and world-wide trends in zooplankton community composition. In Chapter One, data from two long-term monitoring programs in Lake Ontario were used to investigate how the nearshore (5 – 25 m depth) compares to the offshore (> 25 m) habitat. Here, the zooplankton community composition in both habitats had many similar trends over time, including a shift from cyclopoid to calanoid copepods, but the timing, extent, and taxonomic details differed with many changes occurring earlier in the nearshore. In Chapter Two, a few zooplankton-based indicators were selected that summarized detailed community analysis, captured zooplankton community change over time, and may be easier to communicate to a wider audience than zooplankton ecologists. The selected indicators, percent calanoids by biomass and areal density of herbivorous cladocerans, captured changes in vertical distribution and secondary production when reported with lake productivity and total biomass. Lastly, the Zooplankton as Indicators Dataset (ZID) was introduced in Chapter Three. ZID includes data from over 280 waterbodies from around the world and was used to explore the major environmental factors influencing the zooplankton community and found surface temperature, chlorophyll-a, and elevation were predictor variables of the zooplankton community structure. Together, these three chapters expand our understanding of the Great Lakes, test the use of zooplankton as indicators, and provide the building blocks of future world-wide research on zooplankton with a new dataset.