I know at least a couple places where you can buy it (Huis Maria in Harelbeke, Vanuxeem in Ploegsteert, so both Flanders and Wallonia) so I would assume those to be widespread enough throughout the country.
To me coming from France it was Belgium that was the easier place to find glass-bottled water :)
The bottles are reused, and the water tastes a lot better than at least my tap water (in Antwerp - the tap water comes from a stagnant canal used for merchandise shipping, and last year for example it turned green and smelled of algae for a while after a ship carrying fertilizer capsized).
And yeah, you usually give the bottles back. However, it's much more common in Germany than in Belgium, it seems. I have never seen a line to give the bottles back in Gent, unlike Berlin.