The accurate mapping of the basement is one of the most crucial factors in construction of harbour facilities and bridges in the coastal areas. In shallow waters, the seismic reflection method often fails to image the basement geometry beneath the sediment due to reverberation. We present the result of a shallow marine seismic refraction survey using two ships, 12-channel hydrophone arrays deployed on the bottom and a bore-hole sparker or percussion powder as sources. Velocity structure could be computed by tomography algorithm since more than 6 different source points had been applied for one spread. The comparison of the results of the refraction survey with drilling logs demonstrates remarkable consistency in basement geometry. It thus appears that the refraction method in this study is an efficient and cost-effective way to investigate the basement structure in coastal area, river, and lake.