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I'd like to know if you can improve SNR of the signal going to the ADC.

What is the max flow rate if 10 litre/cycle and your sample rate.  It should be about 20 x  the sensor frequency to avoid missing the peak amplitude with light filtering that prevents aliasing with 8 bits and prevents attenuation of the max data cycle rate.  Then you can apply digital filtering (FIR if you want) without averaging which can reduce peak-peak signal amplitude. After you can the data. or compress data as required.

>> What is the envelope detection filter you were mentioning...

This is a H/W method of using +/- envelope tracking with peak and decay times matching buffered and used to track the mean level without the problem of averaging delays.  Then the output comparator uses that which I simulated with Noise and a wandering baseline of 10 mHz or 0.01 Hz.

This simulation assumed the max data rate from the water meter was 1 cycle per second so it can be scaled to match yours.

The detection method can also be done in S/W.

It is much easier to eliminate the noise with a good cable and Hall sensor type/location to get  >= 10:1 signal/noise ratio (SNR) especially when there is spectral overlap.

Here I use an FM sweep signal or a noise data signal to show results. Top right is data+ 0.01Hz noise + white noise

The amplifiers used a ~1 Hz Bessel LPF, then a + peak and decay, -ve peak and decay detector then the average is buffered then inverted again then the filtered input and envelope mean into the comparator.   Averaging is a poor method of filtering if it attenuates the data amplitude and the noise.  That's why the oversampling method is used to prevent aliasing with decimation.

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Filter response test [ATTACH=full]198885[/ATTACH]