New ports are mostly constructed on low lying coastal areas or shallow coastal waters. The quay wall and terminal yard are raised to a level well above mean sea level to assure flood safety. The resulting ‘convention-al terminal’ requires large volumes of fill material often dredged from the sea, which is costly. The terminal yard of a ‘polder terminal’ lies below the outside water level and is surrounded by a quay wall flood defense structure. This saves large amounts of reclamation cost but introduces higher damage potential during flood-ing and thus an increased flood risk. A risk-based framework is made to determine the optimal quay wall and polder level, which is an optimization (cost benefit analysis) under two variables. Overtopping failure proves to be the dominant failure mechanism for flooding. The reclamation savings prove to be larger than the in-creased flood risk demonstrating that the polder terminal could be an attractive alternative to the conventional terminal.