Fish assemblages are an important component of aquatic ecosystems. Present investigation was undertaken to study the Persistence, structure and abundance of fishes from the Ganga river (site 1: Kanpur, site 2: Allahabad and site, 3: Varanasi section), India. The Ganga river is a back bone of Indian fishery. The samples were collected monthly during the period June 2011 to May 2013. Canonical correspondence analysis (CCA) indicated that axis 1 and 2 accounted for 67% and 33% variance for species and environmental relation, respectively. Structure of the fish assemblage of the Ganga at Kanupr to Varanasi harbors of 102 fish species belong to 8 orders and 28 families. 74, 89 and 82 fish species were recorded at Kanpur, Allahabad and Varanasi sites, respectively. Cypriniformes and Cyprinidae were the most rich fish species order and family in all sites. At total stretch, Cypriniformes order was shared 49 species, followed by Siluriformes 26 species and Perciformes 17 species. Orders Clupeiformes shared 5 species. Abundance was dominated by Eutropiichthys vacha compared to Clupisoma garua and Sperata seenghala. According to abundance, Cyprinus carpio var. communis (9.64%) and Oreochromis niloticus (9.19%) were powerfully invader in the Ganga river. Exotic species is alarming for indigenous species biodiversity. C. carpio var. communis and O. niloticus are frequently recorded in the Ganga river. Total hardness, alkalinity and dissolved oxygen were responsible for the presence of Catla catla, Rita rita and Sperata aor, while Labeo calbasu, Cyprinus carpio and Cirrhinus mrigala preferred nitrate, phosphate and total dissolved solid for their abundance. Oreochromis niloticus preferred high biological oxygen demand and lead while Zn and Sulphate were responsible for abundance of L. rohita. For conservation point of view C. carpio var. communis and O. niloticus species should be monitored in the Ganga river. Both species are very harmful for fish biodiversity in the Ganga river. Fish assemblage and their abundance know the health of ecosystem.