A study was carried out to investigate the chronic response of three different cyanobacterial species namely Anabaena fertilissima, Synechocystis sp., and Nostoc muscorum to Pyrene, a high molecular weight (HMW) polycyclic aromatic hydrocarbons (PAHs). Organisms were treated based upon LC50 (lethal concentration at which 50% reduction in growth) concentrations, i.e., 3.0 ppm for Anabaena fertilissima, 3.0 ppm for Synechocystis sp., and 0.5 ppm for Nostoc muscorum as well as finalized one lower and one higher dose to LC50. The influence of pyrene on growth, pigments, release of metabolites, such as carbohydrates, protein, amino acid, and phenols, was carried out. The test doses caused a concentration dependent decrease in carotenoids and phycobilliproteins and showed more sensitivity for pyrene. Depletion of carbohydrate by 47–98% and proteins by 39–81% was encountered with rise in pyrene concentrations after 16th day of exposure in case of high tolerant strain Synechocystis sp. However, phenols were found to rise by 64–93% with increased pyrene concentrations on the contrary, amino acids were reported to decline by 59–93%. The order for the sensitivity of the test species is as follows: Nostoc muscorum > Anabaena fertillissima > Synechocystis sp.