I believe you're combining the Jungle Cruise and the Riverboat - but I could be wrong. The Jungle Cruise boats navigate by the use of a guide bar that extends downward and into a slotted trench/trough in the concrete river bed.
The Riverboat simply uses the rail you see in the above photos. The "trench" that people are referring to is, like someone said, simply the lowest point of the concrete river bed. It appears that the main purpose of having a "lowest point", instead of a flat river bed, is to help with draining the river to certain outlet points. And from the looks of the photos, the trench is obviously working because all the leftover water is sitting in it.