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Who used Water Magic and What was it?
Well first of all, Water Magic was used by the Rhoynar people historically.
Art and music flourished in the cities of the Rhoyne, and it is said
their people had their own magic—a water magic very different from the
sorceries of Valyria, which were woven of blood and fire. Though
united by blood and culture and the river that had given them birth,
the Rhoynish cities were elsewise fiercely independent, each with its
own prince...or princess, for amongst these river folk, women were
regarded as the equals of men.
TWOIAF - Ancient History: 10,000 Ships
It was said that Rhoynar could get intel from Mother Rhoyne about threats and raise Watery Walls to protect their cities:
It was said the Mother Rhoyne herself whispered to her children of
every threat, that the Rhoynar princes wielded strange, uncanny
powers, that Rhoynish women fought as fiercely as Rhoynish men, and
that their cities were protected by "watery walls" that would rise to drown any foe.
TWOIAF - Ancient History: 10,000 Ships
First Turtle War
It was the First Turtle War between Rhoynar and Valyrian Freehold in which Rhoynar made first known use of their magic and flooded Valyrian city of Volon Therys with water, drowning the Valyrian invaders and achieving victory:
The First Turtle War lasted less than a moon's turn. Sar Mell was
raided and burned, yet emerged victorious when Rhoynish water
wizards called up the power of the river and flooded Volon Therys.
Half the city was washed away, if the tales can be believed.
TWOIAF - Ancient History: 10,000 Ships
Pictured, A Rhoynar Turtle fighting Valyrian Dragons (Circa 700 BC, Colorized):

Second Spice War
Then Prince Garin of Chroyane used Water magic extensively against Valyria in Second Spice war. He met initial success, overwhelming three Dragon Lords from Volantis:
Garin found himself facing a hundred thousand foes, a hundred war
elephants, and three dragonlords. Here too he prevailed, though at
great cost. Thousands burned, but thousands more sheltered in the
shallows of the river, whilst their wizards raised enormous
waterspouts against the foe's dragons. Rhoynish archers brought down
two of the dragons, whilst the third fled, wounded. In the aftermath,
Mother Rhoyne rose in rage to swallow Volon Therys. Thereafter men
began to name the victorious prince Garin the Great, and it is said
that, in Volantis, great lords trembled in terror as his host
advanced. Rather than face him in the field, the Volantenes
retreated back behind their Black Walls and appealed to the Freehold
for help.
TWOIAF - Ancient History: 10,000 Ships
Mother Valyria answered her daughter's call and not three, but three hundred Dragonlords arrived from Valyria to turn the tide. They won but the cost was horrible:
And the dragons came. Not three, as Prince Garin had faced at Volon
Therys, but three hundred or more, if the tales that have come down
to us can be believed. Against their fires, the Rhoynar could not
stand. Tens of thousands burned whilst others rushed into the
river, hoping that the embrace of Mother Rhoyne would offer them
protection against dragonflame...only to drown in their mother's
embrace. Some chroniclers insist that the fires burned so hot that
the very waters of the river boiled and turned to steam. Garin the
Great was captured alive and made to watch his people suffer for their
defiance.
[...]
At Chroyane, the cage was hung from the walls, so that the prince
might witness the enslavement of the women and children whose
fathers and brothers had died in his gallant, hopeless war...but the
prince, it is said, called down a curse upon the conquerors,
entreating Mother Rhoyne to avenge her children. And so, that very
night, the Rhoyne flooded out of season and with greater force than
was known in living memory. A thick fog full of evil humors fell, and
the Valyrian conquerors began to die of greyscale.
TWOIAF -
Ancient History: 10,000 Ships
Pictured, Destruction of Garin's Army at hands of Valyrian Dragonlords:

Development of Dornish desert
Later, Nymeria lead her ten thousand ships and landed in Dorne, seeking refuge. While she didn't practice Water Magic herself, some witches came with her who played an important role in development of Dorne:
The Rhoynar brought considerable wealth with them; their artisans,
metalworkers, and stonemasons brought skills far in advance of those
achieved by their Westerosi counterparts, and their armorers were soon
producing swords and spears and suits of scale and plate no Westerosi
smith could hope to match. Even more crucially, it is said the
Rhoynish water witches knew secret spells that made dry streams flow again and deserts bloom.
TWOIAF - Ancient History: 10,000
Ships
Rhoynar wealth, culture and technology gave a cutting edge advantage to the Martells and allowed them to conquer entire Dorne. Current House Martell is officially House Nymeros-Martell, but common usage is just Martell.
Children of Forest
Other than the Rhoynar, it appears that Children of the Forest also practiced a certain form of Water Magic. They used it to break the arm of Dorne, to halt the immigration of the First Men, although too late by that point. But as with most of the legends of Children of the Forest, it is doubtful:
But whether the Breaking took place in a single night, or over the
course of centuries, there can be no doubt that it occurred; the
Stepstones and the Broken Arm of Dorne give mute but eloquent
testimony to its effects. There is also much to suggest that the Sea
of Dorne was once an inland freshwater sea, fed by mountain streams
and much smaller than it is today, until the narrow sea burst its
bounds and drowned the salt marshes that lay between.
Even if we accept that the old gods broke the Arm of Dorne with the
Hammer of the Waters, as the legends claim, the greenseers sang their
song too late.
No more wanderers crossed to Westeros after the Breaking, it is true, for the First Men were no seafarers...but so many of their
forebears had already made the crossing that they outnumbered the
dwindling elder races almost three to one by the time the lands were
severed, and that disparity only grew in the centuries that followed,
for the women of the First Men brought forth sons and daughters with
much greater frequency than the females of the elder races.
TWOIAF - Dorne: the Breaking
Another attempt was made by them in a desperate effort to divide the Continent into two, by breaking it apart on Neck. It didn't succeed however and resulted in only Flooding the Neck and making it a Marshland.
Legend says that the great floods that broke the land bridge that is
now the Broken Arm and made the Neck a swamp were the work of the
greenseers, who gathered at Moat Cailin to work dark
magic.
TWOIAF - Ancient History: the Coming of the First
Men
Instances in current timeline 298-300 AC
No there are no instances of Water Magic being practiced in the current timeline.
As we observed, the art is associated with the Rhoynar and the Children of the Forest.
Children of the Forest are extinct now along with all their arts and magic. Well officially at least, they are still alive up North but even there they haven't shown that power yet. There's however a brief mention of the above-mentioned breaking of the broken Arm of Dorne in AGOT:
"But some twelve thousand years ago, the First Men appeared from the
east, crossing the Broken Arm of Dorne before it was broken. They
came with bronze swords and great leathern shields, riding horses. No
horse had ever been seen on this side of the narrow sea. No doubt the
children were as frightened by the horses as the First Men were by the
faces in the trees. As the First Men carved out holdfasts and farms,
they cut down the faces and gave them to the fire. Horror-struck, the
children went to war. The old songs say that the greenseers used
dark magics to make the seas rise and sweep away the land, shattering
the Arm, but it was too late to close the door. The wars went on
until the earth ran red with blood of men and children both, but more
children than men, for men were bigger and stronger, and wood and
stone and obsidian make a poor match for bronze. Finally the wise of
both races prevailed, and the chiefs and heroes of the First Men met
the greenseers and wood dancers amidst the weirwood groves of a small
island in the great lake called Gods Eye.
AGOT - Bran
VII
As for the Rhoynar, as we saw, they had to flee from advancing Valyrian dragonlords and take refuge in Dorne. It appears however that modern Rhoynar have forgotten the art of their ancestors (Much like remnants of Valyrians have forgotten the art of their ancestors). This is implied as in First Dornish War, Rhoynar didn't use Water Magic against Aegon the Conqueror's dragons. In any case, it was the Rhoynar who were the toughest foes of the Valyrians in their conquest of Essos. And it was again the Rhoynar who proved to be the toughest enemies of Valyrians when Aegon the Conqueror began conquest of Westeros.
Show
No there is no instance of Water Magic being practiced in the Show and nor do I recall any mention of it.