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Glacier retreat is an eminent consequence of exacerbating climate change. In the Svalbard archipelago, most of the glaciers are discharging fresh and turbid waters directly to the sea, substantially impacting the coastal Arctic marine ecosystems. This study attempted to characterise the environmental conditions (hydrography, turbidity, marine aggregates) in the glacial-influenced waters and relate them to the abundance and species composition of protists and zooplankton. The study was conducted in the summer of 2016 in two Svalbard fjords (Wijdefjorden and Rijpfjorden) as well as in coastal waters close to glacier terminations on two islands (Nordaustlandet and Edgeøya). Well-recognised gradients in seawater salinity, turbidity, and particle aggregates that spread from glacier fronts towards open waters were not directly associated with the corresponding horizontal gradients in plankton communities. However, the studied environmental parameters explained the high overall variability in protists and zooplankton abundance (70 and 62% of explained variation, respectively). Different vertical distribution patterns and composition of plankton and marine aggregates were observed between fjords compared to open sea island locations suggesting different origin and transport of pelagic organisms and aggregate suspensions among study locations. The results do not support the hypothesis of synchronised horizontal change in environmental and biological components, which indicates that the relation between glacier meltwaters and plankton dynamics is a derivative of complex interactions driven by several physical and ecological processes that occur at different spatiotemporal scales. Nevertheless, this investigation provides new data pertaining to particle and plankton concentrations and structure in coastal waters near glaciers, which is essential for further understanding of the future coastal Arctic ecosystems functioning under rapid glacier retreat caused by climate change. • Marine-terminating glaciers produce strong environmental gradients in Svalbard waters. • Climate-induced coastal water darkening will create hindered conditions for plankton. • The response of plankton to glacier discharge is not straightforward. • Various spatiotemporal scales result in different bio-physical interactions. • Composition of plankton and aggregates differs between fjords and shelfs of islands. [ABSTRACT FROM AUTHOR]