Zaria, where this Survey was carried out is located in the basement complex of North Central Nigeria. It consists of Precambrian rocks types made up of granite, gneisses and low grade metasediment. The gneiss and the low grade metasediment forms the country rock into which the granitic batholith intruded. This work is meant to examine the effectiveness of joint inversion of refraction tomography and high resolution 3D seismic reflection survey in locating the best point of aquifer within the basement complex. The result of the seismic refraction tomography showed the distribution of seismic velocity within the subsurface with a general increase of velocity with depth. The overburden has an average velocity distribution of 994 m/s. The weathered basement has a velocity range of 1446 to 2912 m/s .The average thickness of the overburden and the weathered basement was found to be 20 m and 9 m respectively. The depth to the fresh was 29 m. 3D surface for both the weathered basement and the fresh basement were generated making use of the X, Y, and Z co-ordinates picked from the reflected seismic events on the individual 2D seismic profiles. The result showed that 3D reflection seismic was able to map-out the structural complexity within the subsurface that change over very little distance, thereby providing a better view of the structural settings within the subsurface. A joint inversion of both methods has proved to be better in the location of the best point for aquifer, than a single method used alone.