Boil it. The bubbles are gas in the water, the boiling should remove the gas so there should be less bubbles. Also bubbles need somthing to form on. Glass is often scratched which gives the gas a place to form the bubble. A very clean or smooth glass surfuce would have many fewer bubbles.
The bubbles are air. So, if you were to remove the air, those bubbles would go away. However, there may still be more air dissolved in the water, so your pump you have to give this a chance to escape too.
Bubbles can be formed because of imperfections in the storage vessel e.g. glass, as well as dust and bits of fibre — this is what happens with champagne!
As for getting rid of them, this is quite hard if you have carbonated water — boil it?
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