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Thanks for sharing such an impressive amount of background research on this issue. We (mWater) have done projects in the past where we used bluetooth to connect a sensor to our app, so that is definitely an option to consider. I also would suggest seriously considering a manual meter that is reported by someone with a smartphone.
Last year, our partner Sparx Engineering built a GPS sensor that tracked the number and distance of trips women made gathering water. Battery life was the key challenge, so we did not go with a cell phone data connection but rather stored the data for two weeks and then downloaded it via bluetooth to the mWater app, which then synchronized it with our server once a connection was available. This works very well when you want to conserve battery life and real time data is not the objective (i.e. M&E applications).
After hearing more about your objectives, the groundwater hydrologist in me thought that you should also consider measuring the depth to water, in order to understand what might be contributing to lower yields in certain dams (such as rapid infiltration versus over-abstraction of water). This can be done using electronic level loggers, but a simple dip meter used by a field worker also works just fine if you don't need high time resolution.
So, given your objectives, I think the manual flow meter approach is worth considering but as you mentioned, most of these meters are designed for municipal piped water, which is very low in dissolved solids and particles. You would need to install a screen ahead of the meter to prevent damage caused by particles of sand or iron from the pump, and clean this out often. I would at least do a pilot test with just a few devices before scaling up the approach.
As far as electronic options, I think WellDone is a good path since they are building a modular system that will soon include an ultrasonic or hall effect sensor for non-intrusive monitoring. You should ask Austin for more information about the data issues, but we have talked several times about building a WellDone integration with the mWater app for data transfer and I would be very interested in moving forward if there was a business case for this.
I also would not put much faith in the charity: water sensor, which is very far behind the announced schedule and still doesn't seem to be available to anyone outside their organization. Also, that sensor is designed to only work on Afridev pumps and requires removal of the pump head for installation. Since your purpose is to perform a representative study, you presumably would want to rotate equipment to different project sites at different times.
Let me know if you have any questions and feel free to get in contract directly john @ mwater.co.