In the latest version of FreeBird, it has become possible to simulate flows in open channels with structures, obstacles, and walls placed at arbitrary locations, as shown in this video. In addition, flow calculations can now be performed for cases where culverts allowing water to pass through are embedded within the structures. As a result, three-dimensional flow analyses under a wide variety of boundary conditions have become possible. Please give it a try.

For details on how to define complex boundary conditions such as those in this example, please see:
https://i-ric.org/yasu/freebird/site/index.html