An understanding of the relationship between the flow generators and harbor design could result in an acceptable seawater renewal into an enclosed basin. The flushing culverts located in the breakwater are the most cost-effective technique for improving water renewal in port engineering. The aim of the paper was to identify and quantify the relation between flow generators and culvert flow to propose an optimal position for the flushing culverts. Mentioned relations are important for designing and positioning the flushing culverts in marinas to achieve optimal sea exchange in the marina basin. Field measurements in the marina Opatija were performed and the data served for calibrating a 3D circulation model and a wave generation/propagation model. The absolute volume of the flow through the culverts caused by wind waves has the more important contribution to the water renewal in the marina basin than the coastal springs have. The optimal flow rates through the culverts are performed by positioning the flushing culvert axis at the mean sea level in accordance with the main incident direction of the propagating waves.Water 2018, 10, 936 2 of 22 discharge, etc.). An understanding of the relationship between the flow generators and harbor design could result in an acceptable seawater renewal with the purpose of reducing pollution concentrations introduced into an enclosed basin [13].Previous scientific research offers mathematical procedures to compute the seawater renewal efficiency of a semi-enclosed basin, frequently grounded either on hydrodynamic or morphological features. Most approaches for seawater renewal estimation are fundamentally built around tidal oscillations as the dominant generator of water circulation inside enclosed basins [14][15][16].The structural features such as the planform geometry of a port, inlet width, water depth, bed slope and so forth, also influence the water renewal efficiency [15][16][17][18]. In regions where the tidal oscillation range is considerably small like the Mediterranean and the Adriatic Sea, the water renewal is also consequently reduced substantially. In these areas, it is widespread to use openings or flushing culverts (pipes or rectangular openings in a breakwater) with the aim of improving the water exchange capacity of the basin [19,20]. Flushing culverts are regarded as the most cost-effective technique for improving water renewal in port engineering. Its purpose is to improve the water renewal within an enclosed basin harnessing also other flow generators like wind and waves, without allowing undesirable wave energy to come into and disturb the port basin. Optimal opening layouts design can be achieved by taking into account two basic yet contradicting criteria, i.e., the water renewal and the wave energy penetration into the harbor [21].Wind action and waves have also been identified to have a significant influence on the seawater renewal. Research making use of numerical models, established to study the Venice lagoon seawater circulation, demonstrated a valuable...