The diversity of cyanobacteria and algae from various microhabitats in Spitsbergen is comparatively well known. However, the relationships between environmental factors and the structure of microflora communities remain largely unclear. This study was conducted in Hornsund Bay, which exhibits large variability in the physicochemical characteristics of habitats, particularly with regard to the availability of nitrogen and phosphorus. This variability, to a large degree, is caused by seabird colonies, which fertilize nutrient-poor terrestrial ecosystems near their nesting areas. The large variations in ecological conditions and vegetation types in the study area aid assessment of habitats representing different combinations of factors potentially influencing the formation of cyanobacterial and algal assemblages. The aim of this study was to examine the influence of physicochemical parameters on the taxonomic composition and diversity of green algae and cyanobacteria (particularly the coccoid, oscillatorialean, and heterocystous taxa). The study encompassed two groups of habitats – soil surface habitats and water-saturated habitats, both characterized by diverse influences of seabird colonies, vegetation cover, and moisture. Our results showed that taxonomic diversity and composition of cyanobacteria and algae were mainly influenced by P–PO<sub>4</sub><sup>3−</sup>, N–NH<sub>4</sub><sup>+</sup> and Ca<sup>2+</sup> (soil surface habitats), and NO<sub>3</sub><sup>−</sup>, as well as moisture (index of wetness) and pH (water-saturated habitats). The variability of these physicochemical properties was largely due to the variability of the seabird colony influence. Taken together, our findings aid in understanding the processes of formation of phycoflora assemblages in Arctic tundra.