Location and Uses
The Wind Waker
In The Wind Waker, Water Jars are primarily used in Dragon Roost Cavern to cool pools of magma, creating temporary platforms of solidified rock to either cross said pools or to ride up spouts of magma to higher ground. Water Jars also appear in the Gohma segment of Ganon's Tower, albeit with no special purpose.
Water Jars, like regular Pots, can also contain items when broken with a Sword, such as Hearts or Arrows. Water Jars are also capable of extinguishing flaming Boko Sticks. When thrown onto Magtails, they immediately curl into balls, temporarily pacifying them.
Four Swords Adventures
Water Jars in Four Swords Adventures appear in a few Stages. In The Mountain Path, they are used to extinguish swaths of flames. In the Lost Woods, a Deku Scrub named Dekki asks for the Links to bring him three different items in order, one of which is a Water Jar. They can be found in houses and caves.