3.5KHz subbottom profiling systems are useful for delineating of shallow (up to 10~100m below the sea bottom) geological structure. These systems are generally used to image geological structures with less than 1m of vertical resolution. However swell in the sea is quite often higher than 1m, causing degradation in the quality of the 3.5KHz subbottom profiles. In this paper, we show the quality of digitally recorded data can be enhanced by the suppression of swell effect. Prior to suppression of swell effect, sea bottom detection procedure was applied using the characteristics that the amplitude of sea bottom reflection is high. To suppress the swell effect, we applied moving average method and high-cut filtering method using the extracted water depth of adjacent traces. Acceptable results were obtained from both methods. In the case of bad quality data or shallow data interfered with direct wave, the suppression of swell effect is difficult due to incorrect sea bottom detection.