Although variability of Arthrospira morphology, widely used in taxonomy and other valuable aspects, as a response to changes in environmental variables has been studied in laboratory cultures, little is known about such responses in the natural habitats. In this study, Arthrospira fusiformis was characterized morphologically in relation to selected environmental variables in the natural ecosystem. Three distinct morphotypes, tightly coiled (H-type), spiral or loosely coiled (S-type), and intermediately coiled (C-type) were observed and described. They varied largely in the degree of coiling, trichome and helix dimensions, coils, shape of trichome end and trichome abundance. The H-type was the most dominant (50%) followed by the S-type (40%). The dominance of H-type and tightening of helix pitch were strongly associated with NO3 − and HCO3 − deficiencies, and high levels of photosynthetically active radiation (PAR) and temperature of the lake. The abundance of S-type was more strongly but negatively related to the high salinity of the lake, probably indicating that decreasing salinity may favor the S-type. In conclusion, the variability in abundance and morphology seem to suggest that A. fusiformis could show morphological modifications in response to environmental stresses in their natural soda lakes, resulting in occurrence of various morphotypes of the same species.