Yeah I agree with respect to the sample rate. I wasn't really sure what sample rate would be best when I started recording the audio, so just picked the highest the soundcard could handle.

I'll definitely look into applying a bandpass filter, thats a good idea!

I had wondered about the spectral signature idea, I was wondering if I could simply slide a window across the data, applying some kind of correlation function, using the magnitude data from the FFT of a known 'bubble' output compared to the window. But I wasn't sure what kind of correlation function to use, whether maybe Pearson correlation coefficient would be sensible?

I like your idea of using multiple microphones to get a 3D visualisation.