Fremyella diplosiphon is a freshwater cyanobacterium that exhibits complementary chromatic adaptation (CCA), which allows the organism to alter its pigmentation and cellular morphology to maximally harvest available green light (GL) and red light (RL) at different depth levels in its aquatic ecosystem. We tested the effect of salinity on CCA-associated pigment and morphological changes in F. diplosiphon. Sodium chloride (NaCl) salt at a concentration of 200mM was found to maximally inhibit growth, chlorophyll levels, and accumulation of phycoerythrin (PE) and phycocyanin (PC) under GL and RL, respectively. NaCl also affected cellular morphology resulting in a larger cell size under both light conditions. Cell length decreased while width increased under GL in the presence of salt, and both cell length and width were increased under RL with salt. The addition of osmoprotectant glycine betaine (GB) to the growth medium in the presence of salt resulted in a reversion of the morphology to that of cells growing in the absence of salt, whereas GB treatment in the presence of salt did not have a major effect on growth or on PE and PC biosynthesis or accumulation. Thus, salt affects cellular morphology due to osmotic stress, while pigmentation is likely affected by ionic toxicity. Understanding the distinct mechanisms of salt-mediated changes on pigmentation and morphology may increase the suitability of strains such as F. diplosiphon, which harbor pigments that allow growth in low light and shaded environments, for adaptation as energy strains.