Water runes in Dungeoneering are used to cast various Magic spells. They can be crafted from rune essence or obtained as a drop from various monsters. 1 type of rune or arrow can be bound to the ammo slot, holding up to 125 (or 225 after completing Salt in the Wound) runes. Water runes are not a recommended bind as catalytic wands and staves provide all elemental runes.
Water runes can be crafted with rune essence at an altar on complexity 3+ dungeons by players with at least level 5 Runecrafting. Each action can use up to 5 essence, with each essence giving more runes based on your Runecrafting level. Make-X in Dungeoneering allows up to 50 actions to be performed, allowing a maximum of 250 essence used. Each crafting action grants 0.6 experience.