Supposedly, they were a dark and vile race of half-men, half-fish creatures, who lurked in the depths of the oceans and harassed the coastlands.
A few maesters speculate that the Deep Ones may have inhabited the Iron Islands before they were settled by the original ironborn - considered an offshoot of the First Men - and that they may have something to do with the mysterious fused black stone ruins which form the foundation of the Hightower in Oldtown - though these are fringe opinions without much support.
In the books
In the A Song of Ice and Fire novels, the Deep Ones are probably mythical and never actually existed - and yet, legends about them (or creatures similar to them) exist all across the known world. According to the legends, the Deep Ones were a "queer, misshapen race of half men sired by creatures of the salt seas upon human women." These horrifying, half-human monsters lived in thrall to demonic gods and ancient beings from the deepest and darkest corners of the ocean.
Diverse legends around the world describe half-human or near-human races from the ocean depths that attacked the coasts in ancient times, or stories which use them to explain the fall of ancient civilizations that left behind only ruins. The different stories often use different names and the descriptions can vary, so it isn't clear if they are describing one race or several similar but unrelated ones, or different offshoots of the same race: other legends about some sort of non-human race or races from the sea refer to "squishers", merlings (mer-people), selkies (seal-men), and walrus-men, among others. All of this is assuming that the legends have any grain of truth behind them whatsoever. It could be that there was one non-human race from the sea and the stories just got distorted over subsequent millennia. Another possibility is that the legends about a dangerous race emerging from the sea are distant cultural memories of some vanished but human race of sea raiders - similarly, some maesters suspect that legends about "centaurs" arose from ancient human tribes who had no knowledge of taming horses, when they saw mounted warriors for the first time.
Yet the fact remains that fairly similar legends about a malignant non-human race from the ocean depths, in service to dark underwater gods, can be found across all three continents of the known world - Westeros, Essos, and Sothoryos - and among peoples separated by such vast distances that they could not possibly have been in contact with each other:
In Westeros, some theorize that the Seastone Chair, throne of the Iron Islands, was carved by some previous race and simply found there when humans first migrated to the region. The theory is that the Deep Ones were the first inhabitants of the islands, which were never home to the two confirmed non-human races from the mainland: the giants don't use boats so they couldn't reach them, and the soil of the isles is too rocky for any Weirwood trees to grow, so the Children of the Forest never settled there either. Therefore the Deep Ones were the only inhabitants of the Iron Islands until the original ironborn (an offshoot of the First Men) arrived and drove them off (if they ever existed). The theory is that similar to how the First Men on the mainland adopted the forest gods of the Children of the Forest, the ironborn's "Drowned God" religion was inspired by the beliefs of the Deep Ones, who - according to the legends - either worshiped or served powerful deities from the black depths of the ocean. The maesters have found no real evidence to support any of this and even the ironborn make no specific mention of the Deep Ones in their cultural history. Still, no one can entirely explain where the Seastone Chair came from. The ironborn usually have a religious explanation for most things about their ancient history: that the legendary Grey King stole fire from the Storm God, made the first boat from a cursed tree, made the first longhall out of the bones of a sea dragon he killed, etc. In contrast, the ironborn have no legendary explanation for where the Seastone Chair came from (i.e. that the Grey King carved it): instead their oral histories just bluntly admit that when they first landed on the islands it was already there.
Farther down the south coast of Westeros, other legends say that the Shield Islands at the mouth of the Mander River were inhabited by merlings and selkies before the First Men arrived and drove them out. "Merling" is the inclusive term for both "Mermaids and Mermen" - half-human on the top half of their bodies but with fish tails on their lower half. This is different from the stories about the Deep Ones, which say that they were horrible half-fish hybrids and only vaguely humanoid. Legends about mermaids and merlings persist across the world - though in this case they are usually made by love-sick sailors who have been out at sea too long and catch glimpse of manatees in the distance. Travelers to the Shivering Sea northeast of Westeros claim that the mermaids they spot have pale skin and black-scaled tails, far more dangerous than the pleasant mermaids of the southern oceans. "Selkie" is a real life term from Celtic mythology, referring to half-men, half-seals (in different versions of the real life myths, they are skinchangers who can transform between human and seal).
Legends about a hostile aquatic race very similar to the "Deep Ones" are found in the folklore of Crackclaw Point, known as "squishers". Crackclaw Point is a large peninsula of pine barrens east of King's Landing whose inhabitants are largely poor holdout families descending from the First Men. Allegedly, the squishers appeared generally human but had larger heads, and scales instead of hair, webbed fingers and toes, and their mouths had multiple rows of green, needle-like teeth. The legends say that the squishers were killed off when the First Men settled the peninsula, but some still frighten bad children by claiming that the squishers will come in the night to snatch them away, eating the boys but saving the girls to breed with and produce more half-fish men. In ancient times, this loathsome race was said to be ruled by the "squisher king", with his horrible unhealed wounds.
In Essos, prominent legends about the ancient civilization of mazemakers that previously inhabited Lorath (in the region of the modern Free Cities) claim that they were destroyed when foes rose up from the sea to destroy them, such as merlings, selkies (seal-men), or walrus-men. This is one of the more prominent legends about the Deep Ones.
Far to the east of Ib, northeast of the Dothraki Sea and off the north coast of the plains of the Jogos Nhai, are a large archipelago called the Thousand Isles: bleak, windswept rocks, some believe they are the only remnants of a kingdom which drowned in ancient times when the sea - or those who dwell within the depths of the sea - rose up to subsume it. The inhabitants of these isles are hostile to all outsiders, and with a forbidding appearance: hairless, with green-tinged skin, and filing their teeth into sharp points. The islanders worship statues and totems to bizarre fish-headed gods, which they set all along their coasts at low tide so they are partially submerged as the sea rises. If the hostile natives manage to capture foreign sailors who set foot on their isles, they kill them in dark rituals held in front of these idols, human sacrifices to their fish-like gods. Curiously, despite living on an island chain these natives live in great fear of the sea, and will absolutely refuse to set foot in the water or on a boat, even on pain of death. Apparently their gods from the depths are not kind, and they do not revere them so much as they fear them, serving as their thralls, and hoping that by sacrificing others they will temporarily sate the hunger of those who dwell in the depths.
Legends similar to the Deep Ones are also found around Sothoryos, in the Basilisk Isles off its northern coast, on the Isle of Toads. Despite the entire continent of Essos and two oceans separating them, the native customs beliefs apparently had some marked similarities with those of the Thousand Isles. There are ancient ruins on the Isle of Toads made by some vanished civilization, with large statues of foul gods set along the coasts. The largest of these is an ancient idol known as the Toad Stone, forty feet high and made of greasy black stone, crudely carved into the shape of a giant toad of malignant aspect. For the most part, the Basilisk Isles have no indigenous inhabitants, with centuries of slaver raids, colonization, and then crippling plagues totally depopulating them, after which they were resettled by the world's worst pirates. The one major exception to this, however, is the Isle of Toads itself: its modern inhabitants are theorized to be descendants of the long forgotten civilization that produced the ruins and the idols. The reason for this suspicion is that the locals don't resemble any other people, but are described as having an unpleasant, fish-like appearance to their faces, with webbed hands and feet.
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