The exchange flow of water and sediment between a harbor and the surrounding waters can be geometrically decomposed into three main components: tidal filling, horizontal, and vertical exchange flows. The method is applied to analyze available measurements at two important harbor basins in Belgium. The geometric analysis can also be applied to the results of a numerical model of hydrodynamics and sediment transport, provided it has sufficient horizontal, vertical, and temporal resolutions to capture the dynamics at the harbor mouth. As such, it can be used as a tool in model calibration. The presented method can provide some insight into the complex relationship (phasing and spatial correlations) between hydrodynamics and sediment concentration that determines harbor siltation.