One of the main challenges in contemporary biological oceanography is to understand the factors that drive the spatial heterogeneity of pelagic organisms. Our study was performed at 10-m depth intervals within the upper 50 m of the ocean, at two different localities on the West Spitsbergen Shelf in the summers of 2009 and 2010. The fine-scale patterns in vertical zooplankton distribution were studied concurrently with measurements of hydrographic and optical properties of the water. We adopted a novel approach to the acquisition of information on light, phytoplankton and particle distributions by in situ measurements with optical sensors. Based on our data, we distinguished specific zooplankton vertical distribution patterns such as the aggregation of Calanus finmarchicus and small copepods toward the surface and the relatively high contribution of C. glacialis to subsurface layers. A vertical separation of Calanus sp. developmental stages was observed, and zones of rather even zooplankton distributions were also found. The variability in zooplankton distribution and community structure was closely related to the hydrographic and optical characteristics of the water; therefore, we hypothesize that these patterns could be the result of fine-scale microhabitat selection by different zooplankton species and life stages.