The seawater intake system is one of the essential operational units in many industries located in the coastal regions. The selection of the type of intake system to a specific sector depends on the total volume required and the quality of the sea water. The offshore seawater intake wells are a suitable option to meet the large volume water requirement and desired water quality. Sometimes two or more intake wells are installed to supply the large volume of the sea water. Since the increase in spacing between the wells leads to an increase in capital cost, it is predominant important to find the optimum distance between the wells. The present study focuses on the external and internal hydrodynamics of two caisson type offshore intake wells situated in random wave environment. Two wells are fabricated in 1:20 model scale and installed in the shallow wave basin and exposed to the random waves. The outer to outer face distance between two wells changed by concerning the outer diameter (D) of the well such that 1D, 1.5D and 2D. The wave run-up, diffraction wave height and free surface water oscillations inside the wells are measured. The distance between the two intake wells has a significant role in wave run-up and free surface oscillation inside the well. Besides, the H/d have a substantial influence on the wave run-up on the seaward face compared to the side and shoreward face in all three cases. Also, the diffraction wave height is minimum when the wells are separated by 1.5D distance. Moreover, wave run-up and free surface water oscillation are optimum when the separation distance between the wells is 1.5D.