Gradual increase in UV-B component reaching earth surface together with heavy metal contamination appears to be a serious environmental concern. Differential sensitivity in photosynthetic characters of Anabaena doliolum, Microcystis sp., and Nostoc muscorum were observed following exposure to UV-B radiation and heavy metals (Cd and Zn) which displayed reduced photosynthesis with maximum inhibition in Anabaena. PSII was the most sensitive component of the electron transport chain depicting 84, 80, and 70 % inhibition in A. doliolum, Microcystis sp., and N. muscorum, respectively. Cadmium and UV-B-induced inhibition of DCPIP photoreduction could not reversed by artificial electron donors in all the strains. However, they substantially reversed the inhibition caused by Zn as well as Zn + UV-B interactively in N. muscorum, not observed in other two strains. Absorption spectra of all the strains showed differential decrement in chl a peak in treated than the control cells (P < 0.25, r = -0.942). Significantly decreased peaks (P < 0.05) by different states of stresses to all the three cyanobacteria were observed in emission spectra. Excitation spectra of the test strains suggest disorganization or delinking of phycobilisomes from the PSII reaction center, also attested by strong negative correlation between the treatment of stress and phycocyanin (P < 0.025, r = -0.971). The present study qualified N. muscorum as most tolerant followed by Microcystis sp., whereas A. doliolum emerged as the most sensitive one and also endorses high toxicity of Cd as compared to Zn.