The effect of salinity (80 and 160 mM) was studied on the photosynthetic apparatus of the native cyanobacterium <i>Fischerella ambigua</i> str. FS 18 over a limited time scale (20, 40, and 60 min). 160 mM salinity for 40 and 60 min had stimulating effects on the photosystem II and phycobilisomes. 80 mM treatment for 20 and 40 min had an excitatory impact on the photosystem and phycobilisome yet were destructive by 60 min for both. The stimulatory and harmful effects of salinity and time are more than that of the sample under conditions without increasing salinity). The photosystem ratios play a key role in damages. 80 mM salinity for 20 min increases the photosystem ratio (PSII : PSI) from 1.24 to 3.28. Similarly, a salinity shock of 160 mM for 20 min reduces the photosystem ratio from 1.24 to 0.34. Photosystem ratios can be determined as pinpointsin the effects of short-time salinity treatments.