Pollution due to oil spilled or scattered in land and sea presents a serious aspect to natural environment. Here, the effect of spilled oil to exert on ecosystem inhabited in the tidal flat is discussed. Spilled oil drifted on the shore adheres to sand beach and penetrates into sand accompanied with the ebbing tide. The penetrated one in sand shields the habitat of benthos, that causes the intercept of the nutrients and the dirt transferred by sea water. The lack of them brings about the decrease of population of benthos. Then there follows also the decrease of the number of water birds, which come flying to the tidal flats to eat benthos. Therefore, these disordered food cycles spoil the function of the tidal flats as purification facilities of the dirt flowing there, which is also feed of benthos. On the other hand, oil penetrated into sand is decomposed into discharged materials by bacteria, main components of which are water and carbon dioxide, that is one of self-defenses which the ecosystem possesses. Such phenomena mentioned above are mathematically modeled into a multi-phase flow formulation with reactions. Flow equations for all phases are unified into a single flow equation to construct a mathematical model. The fictitious domain method plays an important role in this procedure. Also it should be noted that adhesion and penetration as characteristic properties of oil are taken into consideration through boundary conditions of friction type prescribed between oil and sand. Numerical results by solving the mathematical model are presented and compared with experimental results.