The composition of periphyton community on water hyacinth was investigated at Ejirin, part of Epe Lagoon, in relation to environmental characteristics from December 2012 to May 2013. A total of 14,536 individuals of 104 species belonging to five divisions were identified, with Bacillariophyta (82.69%), Cyanobacteria (10.43%), Chlorophyta (5.63%), and Euglenophyta (1.15%). The total species abundance observed showed a strong correlation with rainfall ( ) and strongly significant correlation with TDS ( ; ). Biochemical oxygen demand value remained (BOD) 4.8 mg/L while Shannon-Wiener index value remained ( . The presence of the following organisms could be used as an indicator of environmentally stressed aquatic ecosystem: euglenoids, blue green algae, Nitzschia palea, Surirellasp., Pinnulariasp., Gomphonema parvulum, Mougeotiasp., Spirogyrasp., Trachelomonas affinis(Lemm.), and T. ensifera Daday; T. gibberosaPlayf. and Phormidium articulatum; Lyngbya intermedia; Cymbella ventricosa; Eunotia arcus; Surirella linearisand Closterium parvulumNag.