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Just to confirm Susan, is the water metering using the same magnetic pulse system as the other meter and you are using a Hall sensor in the same way?

One clearly shows a distinct on/off action while the other has many levels. I suspect that is caused by slower passing of the magnet and hence it stopping at differing distances from the sensor.  Perhaps the solution is to use 'delta' measurements rather than absolute ones so you no longer have a high and low threshold but one depending on how much change since the previous reading.  Can you plot that as a graph using the same data as you showed before to see what it looks like?

I'm interested in this because one of the design jobs I will have soon is to measure water flow from a small pumping station (~ 20,000 litres per day) and send the readings to a monitoring system about 0.5Km away. It's like your problem but scaled up 100 times!   I've been thinking of using ultrasonics in view of the large flow, the existing system to be replaced uses magnets on gear wheels but a reed switch to count rotations and it isn't reliable long term.

Brian.