That's a very interesting issue. It it possible to turn off the water for a week to see how much water is lost? Or do you need the pond constantly full for filtration?
Alternatively could you catch the incoming water into a kiddie pool with inflatatable top float ring? So the pond level is maintained but you can see/weigh/measure the new water amount.
Most of the budget flow meters /digital meters have a turbine (propeller) with magnet and an electronic counter. At low flow, the spin rate becomes unreliable with a low viscosity fluid like water.
I am using an inline micro flow meter but it is an add-on to a WiFi valve which has a Zigbee gateway (phone used for real time monitoring and control) so it becomes expensive just for a flow meter. I need to measure 200ml per minute (12 litres per hour) for a constant drip top up-auto water change. It's accurate because it uses positive displacement flow - the meter counts how many times a small chamber is filled and emptied somehow. Unfortunately you can't ramp up the flow rate suddenly on that micro meter past 5 litres per minute but I have dual taps for that.
This is the link for your interest. The WiFi tap itself is excellent.
https://www.link-tap.com/#!/micro-flow-meter