You'd be looking at having a shaft coming out of the water, which imho is a bad idea and a leak waiting to happen.
Two ways you could go around this:
(somehow) build a large prop encased in thin acrylic and use the sensor across this. Might give issues with reflections and refractions.
use the fan sensor. IMHO this is probably the best way to go about a DIY flow meter. This is finding a good sturdy working Hall Effect Sensor circuit from a fan and getting it to work a larger distance from the magnet.
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