The conflict between the wilderness and civilization is most apparent in the descriptions of Jackson's Island, to which Huck initially retreats, and, of course, the mighty Mississippi river down which Huck and Jim make their way. The dangers of the river are often stressed. All manner of boats are wrecked upon it, there are storms and rain, dangerous currents, and so on. It is, obviously, a quite different environment from the polite society of St Petersburg and even from the shoddy towns that line the banks. It is perilous and unpredictable.
Of course, both Huck and Jim are quite well-adapted to such an environment, perhaps precisely because both of them are removed from mainstream civilization - Huck because of his extreme youth and rough upbringing at the very periphery of society and Jim as a slave. The wilderness offers such individuals a degree of liberation from the more oppressive aspects of civilization. Human civilization certainly has its dangers, as seen in this book: deceitful people like the king and duke, the violence of crowds, the deadly feud between the supposedly genteel Grangerfords and Sheperdsons, the ugly institution of slavery. However, the wilderness also brings its own threats.
I think it is particularly illuminating to look at the part of the book where Huck first escapes his abusive father, as well as society itself, to set up camp on the deserted Jackson's Island (Chapter 8)
When it was dark I set by my camp fire smoking, and feeling pretty satisfied, but by-and-by it got sort of lonesome.
He alleviates this loneliness for a while by going down to the riverbank and watching the currents and the stars, but it soon returns. Not until Jim also turns up on the island does he really feel happy:
I was ever so glad to see Jim. I warn't lonesome, now.
Although Huck is relieved to be free from the restrictions of civilization and a mean individual like his father, he can't really do without human company. It is really only his friendship with Jim that makes the long journey down river bearable. This suggests, then, that even someone like Huck, who is generally removed from mainstream civilization, can't really be wholly at one with nature, with the wilderness.
Huck has at least a smattering of civilization; he is not, and never has been completely divorced from human society. Therefore, it makes him feel somewhat uncomfortable to be out in the wilderness all by himself; he begins to find it lonely and rather boring. Human civilization - even a particle of it - is thus seen to be at odds with the wilderness in this story, as exemplified in the character of Huck.