The present study was undertaken to investigate heavy metals in Lake Koka (Ethiopia) food chain and its potential health risk implications. Particularly the study examined the concentration of some heavy metals, their bioaccumulation factors in (water, bottom sediments) and their biomagnifications factors along the food chain of phytoplankton-Zooplankton-muscle tissues of fish species. In situ measurements of the physicochemical parameters (DO, Temperature, EC, and pH) were taken from seven sampling sites using portable Multimeter. The major inorganic nutrients (NO3, NO2, NH3, PO4, and TP) were analyzed in the laboratory using APHA method. The heavy metal analysis was performed using Graphite Furnance Atomic Absorption Spectrophotometer method. The results of the study indicated that the values of most of the physical, chemical and biological parameters such as biological oxygen demand (BOD), chemical oxygen demand (COD), Nitrate (NO3) and Chromium (total Cr) were significantly higher at Modjo downstream site (PCr >Pb>Zn>Cu>Ni>Cd. Metal concentration in the muscle tissue of fish decreased in the sequence of Cr>Cu>Pb>Cd. Bioaccumulation factor of water for Cd and Pb increased as follow phytoplankton > Zooplankton > fish species. The Biomagnifications factor of Chromium for zooplankton, C. garipinus, O. niloticus and C. carpio are 1.63, 1.18, 1.36, and 2.28 respectively. The concentration of Cr was in the direction of fish species >Zooplankton> phytoplankton. The concentration of Cr at Modjo Upstream, Modjo Downstream, and Kentare sites were above the permissible limits. Similarly, the concentration of Pb at the riverine sites was above the permissible limits of WHO and USEPA prescribed. The concentration of Cr on C. garipinus, O. niloticus, and C. carpio was above the permissible Limits of WHO and FEPA. BAFW for (Cd, Pb and Cr) >1) and BAFS for the same metals