In very shallow areas, the frequency by which coastal structures (like dikes and seawalls) are directly broken by large wave forces is low because large waves are broken in deeper areas. The main cause for such destruction is ground scour in front of the structures and outflow of backfilling materials by middle-scale waves; therefore, the scour and the outflow should be considered when designing a coastal structure in a very shallow area. In this paper, a numerical model consisting of CADMAS-SURF, which can calculate fluid motion in porous media, and empirical equations for simulating the outflow phenomena are introduced; thereafter, practical calculations on field cases in Thailand and Japan are demonstrated. Additionally, since the effects of wave periods and water depth to the outflow rate have never been clarified, hydraulic model experiments, empirical calculations using an existing formula, and numerical simulations are performed in order to examine these effects on the outflow rate. The simulated results using the numerical model align well with the experimental results. Moreover, both results show that the outflow rate is proportional to the wave period and inversely proportional to water depth.