It's weird, but sometimes waterways get "corrupted".  The solution is to mine them and place them down again.
In the F4 debug options, turn on "show-debug-info-in-tooltips".  Hover your mouse over the offending water way and see if it is called "straight-water-way" or "straight-water-way-placed".  If it is called just "straight-water-way", then it needs to be mined and rebuilt.
There are two kinds of rails, "straight-water-way" and "straight-water-way-placed".  The mod is supposed to detect when you laying down "straight-water-way" and replaces it with "straight-water-way-placed".  If for some reason it doesn't get replaced, you can't put ships on it (even though they can drive over it).  This usually happens when a different mod tries to copy and paste waterways and doesn't raise the normal player- and robot-building events so cargo ships can replace the rails.  If you get a blueprint with the wrong kind of rails in it, that can cause problems too.
What is your list of mods that you have this problem with?