<p>A method of intaking clean well seawater suitable for farming of marine organisms, etc. through the operation of well drilling of a geological stratum containing a Ryukyu limestone layer, including the steps of (1) selecting a geological stratum having a denatured Ryukyu limestone layer in its intermediate geological stratum as the above geological stratum containing a Ryukyu limestone layer and performing well drilling to a depth below the denatured Ryukyu limestone layer; and (2) intaking only seawater which infiltrates from the depth below the denatured Ryukyu limestone layer.</p>