Glass Bottles are used to hold the potions for brewing. Filling it up from a water source block is more efficient, since filling from a cauldron put the water down 1/3 of the space, thus making it only have 3 uses from a Glass Bottle. If filled via a water source, nothing happens to the block.
Note: N stands for Nothing, G stands for Glass
In a crafting table; Top Row: N,N,N. Middle Row: N,G,N. Bottom Row: G,N,G.