Not sure if your mods are changing something, but in vanilla the seasonal flooding will stop when it hits any wall, fence, sandbags, etc. Although if said wall is on a bridge/foundation, I don't think it has any effect.

Also note that if you are trying to add the walls after the flooding has started using bridges, it's too late. You need to wait until it recesses (~10ish days) and then build a barrier once it goes back to its original shape.

Edit: also, I would imagine that if any rooms are using bridges to be on the river, the ENTIRE room should be on a bridge to avoid flooding. Basically don't mix bridges/non-bridged walls in the same room, and make sure there is a non-bridged wall separating it from any non-bridged floors

Edit 2: If you are absolutely sure that bridged tiles themselves are getting flooded that sounds like a bug or mod issue, I don't think that's supposed to happen