This works fine, I have the same set up in one of my tanks.
You will need to make sure the water level stays high enough to cover the heater, both with and without the waterfall running. If you are using a glass one and it is not emersed it can break from thermal shock.
And think about access to it. If it malfuntions or you want to change the temp with the seasons, are you going to have to break down the tank to get to it?
(Personally I just sealed mine in, and I unplug it in the summer and plug it back in in the fall.) (Funny story about that: The first fall I forgot to plug it back in, and then I couldn't figure out why my normally bold azureus darts were hidding all the time. Luckily I got some good advice to check temps, and figured it out from there.)
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