Climate-induced glacial retreat in the Arctic results in an increased supply of meltwater with suspended terrigenous material into the marine environment. Despite increasing research efforts, effects of glacial retreat on functioning of plankton are not well documented and understood. Thus, we studied a hydro-optical seawater regime along with particle/plankton concentrations and composition structure in a high Arctic fjord (Isfjorden, West Spitsbergen) during mid-summer in 2019. This comprehensive study of the upper 50m water layer presented a sharp distinction between 'muddy' waters influenced by glacial and river runoff and 'clear' open fjordic waters in the form of a notable difference in chlorophyll a concentrations, extent of euphotic zone depth, turbidity, inorganic/organic particle concentrations, and water colour. In this study, we present that the effects of glacial retreat on Arctic pelagial depend not only on different types of glaciers (marine- and land-terminating), but presumably, also on fjord topography and exposure to oceanic water inflow. The contrasting glacial, hydrological, and topographical conditions had different effects on the share of zooplankton and marine snow. Despite adaptation of the planktonic communities in the Arctic to high sediment loads and resultant light limitations, our study shows that continuing retreat of tidewater glaciers will have negative effect on planktonic communities especially in enclosed shallow fjord branches. Moreover, seawater darkening due to high turbidity could negatively affect tactile predators, such as gelatinous zooplankton. Additional division of plankton into functional groups typically used in the biogeochemical models demonstrated that diatoms, flagellates and mesozooplankton are influenced by suspended matter, whereas microzooplankton are highly adaptive to increased sediment loads. Since we investigated the largest Svalbard fjord system and incorporated multiple components of the pelagic realm, the current study delivers important recommendations for including marine snow and gelatinous zooplankton in ecosystem models applied in polar regions.