The retreat of glaciers, melting of permafrost, and increased riverine runoff influence Arctic fjords and their physical and biological environment, but to which extent is poorly known. In this study, I determined the impact of glacial and riverine inputs on the Arctic zooplankton community composition in the largest fjord system in Svalbard, Isfjorden, at 78°North. The physical (temperature, salinity, turbidity, Secchi depth) and biological (chlorophyll a) environment were carefully studied seasonally and spatially from the start to the outer end of the three fjord arms of Isfjorden: Billefjorden, Tempelfjorden, and Adventfjorden in May, June and August 2018. The most prominent spatial and seasonal pattern across all fjords was the high contribution of meroplankton to the total zooplankton community. High total (~14.000 ind. m-3) and relative abundance (>50%) of meroplankton were documented at the innermost sites in May, which decreased along the salinity gradient from inner to outer. Meroplankton also showed a clear seasonal shift from cirriped nauplii and cypris in May and June, to bivalve veliger in August. Holoplankton shifted from copepodite stages and adult larger sized copepods, Calanus spp. in particular, in May and June, to a dominance of the smaller cyclopoid copepod Oithona similis in August. In addition, copepod nauplii dominated at the innermost sites in May relative to the total holoplankton (~70%) and decreased along the salinity gradient from inner to the outer fjord. The trophic modes of zooplankton did not show any clear spatial pattern but shifted seasonally from predominantly herbivores in May to omnivores to August. The zooplankton biomass did not show any significant differences between the months, nor the habitats. However, the species diversity increased from inner to outer in all three months, presumably affected by environmental stress at the innermost sites. By implementation of ordination methods, seasonality was identified as the most important driver of the zooplankton communities, where temperature, salinity, and light availability was shown to explain the most variation. The study also supported that terrestrial input has an impact on the zooplankton communities, in accordance with previous research. The study of zooplankton in coastal areas helps to understand the undergoing changes in these ecosystems. In order to gain more knowledge on future changes in the Arctic, future studies highlighting these subjects are recommended.