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Ny-Ålesund in Svalbard is a complex area with both continental and tidal glaciers. There are a lot of studies on prokaryotic and eukaryotic communities in coastal water and soil, but without studies in glacial-related waters. We make a distinctive and consolidated study on the structure of the prokaryotic and eukaryotic communities of pure glacial meltwater, glacial melting lake, glacial meltwater flowing via different types of soil at various elevations, estuarine glacial water and marine water. Moreover, we analyze the environmental–microbial relationships of the prokaryotic and eukaryotic communities via a canonical correspondence analysis and redundant analysis compared by a Pearson analysis. We found that there were distinct microbes in different environments. Altitude had significant correlations with prokaryotic and eukaryotic species in the 12 water samples (ppro = 0.001, npro = 1010, and peuk = 0.012, npro = 1651) (Pearson analysis). Altitude, temperature and salinity, respectively, accounted for 28.27%, 10.86% and 8.24% in the prokaryotic community structure and 25.77%, 17.72% and 3.46% in the eukaryotic, respectively, in water. Nitrogen, silicate and pH accounted for 38.15%, 6.15% and 2.48% in the prokaryotic community structure in soil and 26.65%, 12.78% and 8.66% in the eukaryotic. Eukaryotes were more stable than prokaryotes in changing environments. Cyanobacteria and dinoflagellates better adapt to a warming environment. Gammaproteobacteria and Chrysophysceae were most abundant in soil. Alphaproteobacteria, Bacteroidia, Mamiellophyceae and Prasinophytae were most abundant in water. Within these microbes, Bacilli and Chlorophyceae were only found in glaciers; Actinobacteria, KD94-96, Thermleophilia, Embryophyta, Trebouxiophyceae and Sordariomycetes were unique to soil.