New ports are mostly constructed on low lying coastal areas or in 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 ‘conventional terminal’ requires large volumes of good quality fill material often dredged from the sea, which is costly. The alternative concept of a ‘polder terminal’ has a terminal yard which lies below the outside water level and is surrounded by a quay wall flood defence structure. This saves large amounts of reclamation investment but introduces a higher damage potential in case of flooding and corresponding flood risk. Important conditions for the feasibility of a polder terminal are low pervious subsoil and high reclamation cost. Further, a polder terminal requires a water storage and drainage system, against additional cost. A risk-based analysis of the optimal quay wall height and polder level is performed, which is an optimization (cost benefit analysis) under two variables. The overtopping failure mechanism proves to be the dominant failure mechanism for flooding. During overtopping the water depth in the polder terminal is larger than on the conventional terminal, resulting in higher damage potential and corresponding flood risk for the polder terminal. However, the reclamation savings prove to be larger than the increased flood risk: the ‘polder terminal’ could save 10 to 30% of the total cost (investment and risk) demonstrating that it to be an economically attractive alternative to a conventional terminal.