The geometry of estuaries is often altered through dredging to make room for ships and with extensive landfill over wetlands to enable development. Here, we use historical maps to help create computational models of seawater flow around and into a lagoonal bay of New York City for the 1880s and 2010s. Our results show that these past man-made changes cause higher coastal storm tides and that they result specifically from deeper depths, expanded inlet width, and landfill.