Capital works projects, particularly the modification of coastal rivers, are becoming increasingly significant to economic activities worldwide as a response to climate-driven changes and urbanization. The benefits of channel modification projects can be realized quickly, but the altered movement of sediments in the river channel can lead to unintended morphologic changes decades later. An example of this is the closure of the San Bernard River mouth, located on the central coast of Texas, which was clogged by sediments in the 1990s as a result of two major projects in the area: the diversion of the Brazos River channel (1929) and the construction of the Gulf Intracoastal Waterway (GIWW) (1940s). The objective of this study was to document the delayed geomorphic response to the projects using historical aerial imagery and provide a snapshot of flow pathways in the area using measurements collected in situ. Results showed that the GIWW was the main conduit for river flow as it bisects the San Bernard 2 km inland of its river mouth, reducing discharge in the terminal limb of the river. Due to reduced flow, the river mouth became clogged with wave-transported sediment supplied the Brazos River which had been diverted to within 6 km of the San Bernard. With no connection to the sea, altered sediment and flow pathways have led to numerous hazards and costly corrective dredging projects. To optimize the cost-effectiveness of channel modification projects their long-term impact must be considered as managers continue to adapt to ever-changing coastal zones.