Marine microbial plankton drive global biogeochemical cycles and are therefore pivotal to the ecosystem functioning of the biosphere. In particular marine picoplankton harbour a vast biodiversity on which their community dynamics and functioning are based. Because they function collectively as a community, it is crucial to understand the underlying diversity patterns of microbial assemblages and identify their drivers. The data set I investigated here allows insights into surface water bacterio- and picoplankton communities of Arctic and subarctic coastal waters and fjord systems. To infer their diversity with a metabarcoding approach, I amplified and sequenced the V4 regions of the prokaryotic 16S and eukaryotic 18S ribosomal DNA which serve as molecular markers. The resulting amplicons were arranged into amplicon sequence variants (ASVs) which I used as a substitute for species. In comparing prokaryotic and picoeukaryotic alpha and beta diversity across space, I unveiled profound differences between the domains, the investigated regions and the respective drivers. Picoeukaryotes appeared to vastly exceed prokaryotes in their richness and are thus hypothesized to comprise a large rare biosphere ensuring community stability. They are more strongly influenced by fjord structures and glaciers than prokaryotes and I found spring bloom conditions to induce a drastic decrease in picoeukaryotic richness. Prokaryotes appeared to be more strongly influenced by nutrient availability and environmental conditions than picoeukaryotes, resulting in a higher spatial turnover through more efficient taxa sorting. I found no distance-decay relationship in prokaryotic and picoeukaryotic communities on the scales observed here. I assume a functional coupling and mutual dependence of the prokaryotic and eukaryotic communities based on co-varying alpha diversity measures, which were fundamentally restructured by spring bloom conditions. I observed a pronounced compositional turnover in both space and time. Seasonal succession and change across years appeared to shape picoplankton communities equally strong as spatially differing influences, stressing the need to control for time in future spatial analyses. In contributing to a better understanding of the basic patterns and their drivers underlying picoplankton diversity, this study may also contribute to a better understanding of the impact climate change will have on the planet. Spatial dynamics across environmentally differing sites can deliver indications to the influence of environmental changes in time. Thus, they allow to anticipate changes in microbial plankton dynamics and therefore the functioning of the global biosphere in the face of climate change.