Abstract: A numerical model based on the insitu measured topographic data was implemented, using the unstructuredgrid, threedimensional primitive equation, finitevolume coastal ocean model (FVCOM) including a dikegroyne module, for the study of temporal and spatial variations of overtopping flow at the south leading jetty constructed in the deep waterway channel. We investigated the temporal and spatial changes of overtopping flow by computing crosssection water flux before and after the project. The hydrodynamic condition around the north passage showed noticeable changes after the building of dikes and groynes. After the construction, respectively, net lateral current between the two channels points to the north passage with a relatively large amount of discharge. As estimated, spatially varying unit width net overtopping water flux had a significant feature, which was bounded at the corner, showed that the flux increased gradually at the upper half and decreased at the latter with a larger value. On a time scale the amplitude appeared no remarkable changes seasonally but on the other hand paced periodically in a tidal cycle. Moreover, the results showed a strong linear correlation between net water flux and tidal level.