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Further to the suggestion of a 'PD' meter, an orifice plate meter should be able to cope with the water quality, and can be quite cheap and cheerful, if you get it machined up to your design, which would probably be about as accurate as a rotameter. The meter when connected to a manometer does not require any electrical gubbins. A 'pukka' metering version will be much more expensive, but also more accurate and rather more sensitive to blockage. I think that as long as you design your system so that you can flush out the tappings and get access to clean the inside of the orifice installation it could be practical, although requiring periodic maintenance.

Orifice meters do have a significant headloss and are sensitive to disturbance in the flow and so require quite long straight lengths of pipe upstream and downstream of the meter location.