(Not sure where the 3D print thought comes from - maybe the visual included by the OP which I only interpret as a design layout, not a print model. I could be wrong.
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Assuming you are using Blue Moon's fantastic Chicago buildings? Yes or no?
Either way, my approach would be to use underlayment, about a 1/4" thick material similar to plywood. Create a sandwich of this material using 1" x 1" hardwood as the separators. Glue and screw, countersink the screws, putty, smooth, allow to dry and sand. For the port area, jigsaw out the actual port (edit: only jigsaw the top layer of underlayment, the 'top' of the bottom piece will be the 'water' surface)and use well placed 1x1 material to support, can use shaped insulation foam covered with spackling compound wherever there is no 'wall' between street level and water level.
Because the material is thin, the board's will be pretty light but with the hardwood separators glued and screwed, it should remarkably strong. Using care building by this method, you should not end up with 'warping' so not 'fault' lines to worry about. But always store flat just in case.
Underlayment comes in 4'x8' sheets locally so it does need to be cut to size. If you can, have a Big Box store cut it to size with their large cutting tools. A lot easier and more reliable and accurate than cutting such a large sheet on a table saw at home - if you had one.
Oh, underlayment is used as a base for laying flooring material in some applications thus its name.
Look forward to seeing your project develop. And really, really want to see what sort of vehicles you come up with!
Best of luck with your project.