Samples of fish organs, sediment and water were collected from five sampling sites of Lakes Awassa and Ziway. A procedure consuming 13 mL mixture of HNO 3 -HClO 4 -H 2 O 2 for intestine and sediment or 5.0 mL mixture of HNO 3 -H 2 O 2 for scale, spleen and bile for digestion of freeze-dried fish organs (except bile) and sediment was developed. Concentrations of eight metals were determined using flame atomic absorption spectrophotometer. Concentrations of metals in bile, intestine, scale, spleen and sediment varied (mg/kg): Cd 0.83-13.41, 2.67-5.01, 4.46-13.24, 2.58-6.66, 3.19-10.51, respectively; Cr 0.79-4.27, 1.13-5.09, 2.13-5.74, 0.47-1.36, 4.14-8.66, respectively; Co 0.51-1. 19, respectively; respectively; respectively; respectively; respectively; respectively. Most of the elements in water samples occurred below detection limit. The pattern for concentrations of trace metals followed: sediment > scale > intestine > bile > spleen > water. Using a ternary plot, positive correlation was observed for the specific fish organ with the sediment and water samples. There was no significant difference between the two lakes in accumulating trace metals however Lake Awassa had higher concentration.