In the Arctic Ocean copepods transfer energy produced by autotrophs to higher trophic levels. Net tows have long been used as the main zooplankton sampling tool but can hardly indicate the abundance and distribution of these animals on a fine-scale level. The LOKI (Lightframe On-sight Keyspecies Investigation) is an in-situ optical underwater imaging device capable of recording the vertical distribution of zooplankton at a scale of ~30-60 cm. Using this device, the fine-scale distribution of the key herbivorous copepods Calanus glacialis and C. hyperboreus as well as that of the omnivore Metridia longa was analyzed. It was investigated how the fine-scale vertical distribution of copepods was coupled to fluorescence of microalgae during the phytoplankton bloom and how that pattern differed between eastern and western North Water Polynya. Eastern and western NOW showed substantial differences in the fluorescence of microalgae which seemed to influence the fine-scale copepod distribution. Whereas copepod abundance and fluorescence seemed almost vertically separated on the Canadian side of the polynya, the abundance of the same taxa showed a strong vertical coupling with fluorescence on the Greenland side. The results suggest a strong influence of physical parameters in the NOW (e.g. temperature and upwelling), likely governed by the West Greenland Current and Baffin Island Current, on microalgae and hence fine-scale zooplankton distribution.