Europeans encountered natives with their own Native American Gods. There was no one native religeon.
Our special project presenting the definitive account of France in Canada by Francis Parkman, one of America’s greatest historians.
Each primitive Indian has his guardian manitou, to whom he looks for counsel, guidance, and protection. These spiritual allies are gained by the following process. At the age of fourteen or fifteen, the Indian boy blackens his face, retires to some solitary place, and remains for days without food. Superstitious expectancy and the exhaustion of abstinence rarely fail of their results. His sleep is haunted by visions, and the form which first or most often appears is that of his guardian manitou, — a beast, a bird, a fish, a serpent, or some other object, animate or inanimate. An eagle or a bear is the vision of a destined warrior; a wolf, of a successful hunter; while a serpent foreshadows the future medicine-man, or, according to others, portends disaster.  The young Indian thenceforth wears about his person the object revealed in his dream, or some portion of it, — as a bone, a feather, a snake-skin, or a tuft of hair. This, in the modern language of the forest and prairie, is known as his “medicine.” The Indian yields to it a sort of worship, propitiates it with offerings of tobacco, thanks it in prosperity, and upbraids it in disaster.  If his medicine fails to bring the desired success, he will sometimes discard it and adopt another. The superstition now becomes mere fetich-worship, since the Indian regards the mysterious object which he carries about him rather as an embodiment than as a representative of a supernatural power.
[1 Compare Cass, in North-American Review, Second Series, XIII. 100. A turkey-buzzard, according to him, is the vision of a medicine-man. I once knew an old Dahcotah chief, who was greatly respected, but had never been to war, though belonging to a family of peculiarly warlike propensities. The reason was, that, in his initiatory fast, he had dreamed of an antelope, — the peace-spirit of his people.
Women fast, as well as men, — always at the time of transition from childhood to maturity. In the Narrative of John Tanner, there is an account of an old woman who had fasted, in her youth, for ten days, and throughout her life placed the firmest faith in the visions which had appeared to her at that time. Among the Northern Algonquins, the practice, down to a recent day, was almost universal.]
[2 The author has seen a Dahcotah warrior open his medicine-bag, talk with an air of affectionate respect to the bone, feather, or horn within, and blow tobacco-smoke upon it as an offering. “Medicines” are acquired not only by fasting, but by casual dreams, and otherwise. They are sometimes even bought and sold. For a curious account of medicine-bags and fetich-worship among the Algonquins of Gaspé, see Le Clerc, Nouvelle Relation de la Gaspésie, Chap. XIII.]
Indian belief recognizes also another and very different class of beings. Besides the giants and monsters of legendary lore, other conceptions may be discerned, more or less distinct, and of a character partly mythical. Of these the most conspicuous is that remarkable personage of Algonquin tradition, called Manabozho, Messou, Michabou, Nanabush, or the Great Hare. As each species of animal has its archetype or king, so, among the Algonquins, Manabozho is king of all these animal kings. Tradition is diverse as to his origin. According to the most current belief, his father was the West-Wind, and his mother a great-granddaughter of the Moon. His character is worthy of such a parentage. Sometimes he is a wolf, a bird, or a gigantic hare, surrounded by a court of quadrupeds; sometimes he appears in human shape, majestic in stature and wondrous in endowment, a mighty magician, a destroyer of serpents and evil manitous; sometimes he is a vain and treacherous imp, full of childish whims and petty trickery, the butt and victim of men, beasts, and spirits. His powers of transformation are without limit; his curiosity and malice are insatiable; and of the numberless legends of which he is the hero, the greater part are as trivial as they are incoherent.  It does not appear that Manabozho was ever an object of worship; yet, despite his absurdity, tradition declares him to be chief among the manitous, in short, the “Great Spirit.” [“Presque toutes les Nations Algonquines ont donné le nom de Grand Ličvre au Premier Esprit, quelques-uns l’appellent Michabou (Manabozho).” — Charlevoix, Journal Historique, 344.] It was he who restored the world, submerged by a deluge. He was hunting in company with a certain wolf, who was his brother, or, by other accounts, his grandson, when his quadruped relative fell through the ice of a frozen lake, and was at once devoured by certain serpents lurking in the depths of the waters. Manabozho, intent on revenge, transformed himself into the stump of a tree, and by this artifice surprised and slew the king of the serpents, as he basked with his followers in the noontide sun. The serpents, who were all manitous, caused, in their rage, the waters of the lake to deluge the earth. Manabozho climbed a tree, which, in answer to his entreaties, grew as the flood rose around it, and thus saved him from the vengeance of the evil spirits. Submerged to the neck, he looked abroad on the waste of waters, and at length descried the bird known as the loon, to whom he appealed for aid in the task of restoring the world. The loon dived in search of a little mud, as material for reconstruction, but could not reach the bottom. A musk-rat made the same attempt, but soon reappeared floating on his back, and apparently dead. Manabozho, however, on searching his paws, discovered in one of them a particle of the desired mud, and of this, together with the body of the loon, created the world anew. 
[1 Mr. Schoolcraft has collected many of these tales. See his Algic Researches, Vol. I. Compare the stories of Messou, given by Le Jeune (Relations, 1633, 1634), and the account of Nanabush, by Edwin James, in his notes to Tanner’s Narrative of Captivity and Adventures during a Thirty-Years’ Residence among the Indians; also the account of the Great Hare, in the Mémoire of Nicolas Perrot, Chaps. I., II.]
[2 This is a form of the story still current among the remoter Algonquins. Compare the story of Messou, in Le Jeune, Relation, 1633, 16. It is substantially the same.]
There are various forms of this tradition, in some of which Manabozho appears, not as the restorer, but as the creator of the world, forming mankind from the carcasses of beasts, birds, and fishes.  Other stories represent him as marrying a female musk-rat, by whom he became the progenitor of the human race. 
[1 In the beginning of all things, Manabozho, in the form of the Great Hare, was on a raft, surrounded by animals who acknowledged him as their chief. No land could be seen. Anxious to create the world, the Great Hare persuaded the beaver to dive for mud but the adventurous diver floated to the surface senseless. The otter next tried, and failed like his predecessor. The musk-rat now offered himself for the desperate task. He plunged, and, after remaining a day and night beneath the surface, reappeared, floating on his back beside the raft, apparently dead, and with all his paws fast closed. On opening them, the other animals found in one of them a grain of sand, and of this the Great Hare created the world. — Perrot, Mémoire, Chap. I.]
[2 Le Jeune, Relation, 1633, 16. — The musk-rat is always a conspicuous figure in Algonquin cosmogony.
It is said that Messou, or Manabozho, once gave to an Indian the gift of immortality, tied in a bundle, enjoining him never to open it. The Indian’s wife, however, impelled by curiosity, one day cut the string, the precious gift flew out, and Indians have ever since been subject to death. Le Jeune, Relation, 1634, 13.]
Searching for some higher conception of supernatural existence, we find, among a portion of the primitive Algonquins, traces of a vague belief in a spirit dimly shadowed forth under the name of Atahocan, to whom it does not appear that any attributes were ascribed or any worship offered, and of whom the Indians professed to know nothing whatever;  but there is no evidence that this belief extended beyond certain tribes of the Lower St. Lawrence. Others saw a supreme manitou in the Sun.  The Algonquins believed also in a malignant manitou, in whom the early missionaries failed not to recognize the Devil, but who was far less dreaded than his wife. She wore a robe made of the hair of her victims, for she was the cause of death; and she it was whom, by yelling, drumming, and stamping, they sought to drive away from the sick. Sometimes, at night, she was seen by some terrified squaw in the forest, in shape like a flame of fire; and when the vision was announced to the circle crouched around the lodge-fire, they burned a fragment of meat to appease the female fiend.
[1 Le Jeune, Relation, 1633, 16; Relation, 1634, 13.]
[2 Biard, Relation, 1611, Chap. VIII. — This belief was very prevalent. The Ottawas, according to Ragueneau (Relation des Hurons, 1648, 77), were accustomed to invoke the “Maker of Heaven” at their feasts; but they recognized as distinct persons the Maker of the Earth, the Maker of Winter, the God of the Waters, and the Seven Spirits of the Wind. He says, at the same time, “The people of these countries have received from their ancestors no knowledge of a God”; and he adds, that there is no sentiment of religion in this invocation.]
The East, the West, the North, and the South were vaguely personified as spirits or manitous. Some of the winds, too, were personal existences. The West-Wind, as we have seen, was father of Manabozho. There was a Summer-Maker and a Winter-Maker; and the Indians tried to keep the latter at bay by throwing firebrands into the air.
When we turn from the Algonquin family of tribes to that of the Iroquois, we find another cosmogony, and other conceptions of spiritual existence. While the earth was as yet a waste of waters, there was, according to Iroquois and Huron traditions, a heaven with lakes, streams, plains, and forests, inhabited by animals, by spirits, and, as some affirm, by human beings. Here a certain female spirit, named Ataentsic, was once chasing a bear, which, slipping through a hole, fell down to the earth. Ataentsic’s dog followed, when she herself, struck with despair, jumped after them. Others declare that she was kicked out of heaven by the spirit, her husband, for an amour with a man; while others, again, hold the belief that she fell in the attempt to gather for her husband the medicinal leaves of a certain tree. Be this as it may, the animals swimming in the watery waste below saw her falling, and hastily met in council to determine what should be done. The case was referred to the beaver. The beaver commended it to the judgment of the tortoise, who thereupon called on the other animals to dive, bring up mud, and place it on his back. Thus was formed a floating island, on which Ataentsic fell; and here, being pregnant, she was soon delivered of a daughter, who in turn bore two boys, whose paternity is unexplained. They were called Taouscaron and Jouskeha, and presently fell to blows, Jouskeha killing his brother with the horn of a stag. The back of the tortoise grew into a world full of verdure and life; and Jouskeha, with his grandmother, Ataentsic, ruled over its destinies.
[The above is the version of the story given by Brébeuf, Relation des Hurons, 1636, 86 (Cramoisy). No two Indians told it precisely alike, though nearly all the Hurons and Iroquois agreed as to its essential points. Compare Vanderdonck, Cusick, Sagard, and other writers. According to Vanderdonck, Ataentsic became mother of a deer, a bear, and a wolf, by whom she afterwards bore all the other animals, mankind included. Brébeuf found also among the Hurons a tradition inconsistent with that of Ataentsic, and bearing a trace of Algonquin origin. It declares, that, in the beginning, a man, a fox, and a skunk found themselves together on an island, and that the man made the world out of mud brought him by the skunk.
The Delawares, an Algonquin tribe, seem to have borrowed somewhat of the Iroquois cosmogony, since they believed that the earth was formed on the back of a tortoise.
According to some, Jouskeha became the father of the human race; but, in the third generation, a deluge destroyed his posterity, so that it was necessary to transform animals into men. — Charlevoix, III. 345.]
– The Jesuits in North America in the Seventeenth Century Introduction by Francis Parkman
These were some of the Native American Gods.
The below is from Francis Parkman’s Introduction.
If, at times, it may seem that range has been allowed to fancy, it is so in appearance only; since the minutest details of narrative or description rest on authentic documents or on personal observation.
Faithfulness to the truth of history involves far more than a research, however patient and scrupulous, into special facts. Such facts may be detailed with the most minute exactness, and yet the narrative, taken as a whole, may be unmeaning or untrue. The narrator must seek to imbue himself with the life and spirit of the time. He must study events in their bearings near and remote; in the character, habits, and manners of those who took part in them, he must himself be, as it were, a sharer or a spectator of the action he describes.
With respect to that special research which, if inadequate, is still in the most emphatic sense indispensable, it has been the writer’s aim to exhaust the existing material of every subject treated. While it would be folly to claim success in such an attempt, he has reason to hope that, so far at least as relates to the present volume, nothing of much importance has escaped him. With respect to the general preparation just alluded to, he has long been too fond of his theme to neglect any means within his reach of making his conception of it distinct and true.