At the design stage of a ship, the engine output is determined by taking into consideration of a lowering of performance. The lowering is mainly caused by winds, waves, aging deterioration and biological fouling. To keep the speed in actual seas, the output is appended to a proper ratio, which is called sea margin. The component of sea margin divides into two groups. One is a weather effect and the other is a deterioration effect which progresses with time. For the estimation of the weather effect, weather forecasting data of 8 years were applied. Also, for the estimation of the deterioration effect, roughness increase of the hull was taken into account. In this paper, the desirable sea margin is derived rationally. As an example, for a coastal chemical tanker, Shinko Maru No.28, performance estimation and voyage data analysis were carried out. By comparison with the estimated and analyzed sea margin, it made clear that the estimated sea margin agrees with the analyzed one. Consequently the physical meaning of sea margin is explained as a function of wave, wind and time.