I was doing that, but it failed. The doors to the ride only opened once and after that it stayed shut, with a very long queue waiting.
I have done it using rocks to block up all the space around the tracks rather than proper gates. It is possible, my boat track runs through habitats with about 13 species having access to the water.
The rocks you have just below the surface - they block animals but allow boats through? Do you use null barriers with that?
Here you can see the riverboat ride, it travels around the whole african area, pretty much every habitat uses the same water, except the cheetah at the top because the hippos have most of that (I use a glass barrier in the water to divide).
This is an example of a two lane rock gate, they are 100% effective at stopping anything big but have had some plucky baby zebra make a run for it.