The East African Rift system is part of a very prominent landmark on the surface of the Earth. While passing through Ethiopia, it approximately cuts it in to two-thirds and one-thirds in the north- western side and south-eastern side respectively forms very distinct land features. The Rift system in Ethiopia is divided into three parts: the Afar-Danakil Depression in the north-east, the Main Ethiopian Rift in the middle and the South/western Rift in the south/west. The Central Main Ethiopian rift is the concern of the study area which can be named as the lakes regions. The geophysical investigation of hydraulic connection between Koka and Ziway ?Shala basins revealed that the setting of the subsurface geological structure; especial the fault zones and fractures due to tensile stress have role in ground water flow between the two basins (koka and Ziway-Shala basins). The study was also important in economic development of region in ground water exploration and exploitation for the society.