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The show has a lot of elements explained only in the novels:
- Jon deals with one wight (Othor) in "The Pointy End", but nothing is ever said of the other one (Jafer Flowers) brought back at the same time. In the books, that wight kills Ser Jaremy Rykker in the yard before finally being hacked to pieces by the rest of the Watch.
- In the books, Drogo removes Mirri Maz Duur's poultice and relies on his traditional remedies instead, lending some credence to Mirri (who criticized the Dothraki methods) when his wound gets infected. In the TV series, they only use Mirri's method and Drogo gets infected anyway, yet Daenerys still trusts her to heal him again.
- Sansa refuses to escape King's Landing with the Hound in "Blackwater", as she does in the books. However, in the books the Hound is menacing to the point of a Near-Rape Experience and Sansa already has her own escape plan, neither of which are in the show, which leaves her with no real reason to refuse.
- In the books, Barristan catches up to Daenerys at the end of her extended stay in Qarth, after word of her presence has spread extensively along the trade routes. In the show, she's just arrived in Astapor, making it a much more Contrived Coincidence that Barristan happens to be there, especially since Astapor is only a backwater port for slaves while the heavy traffic to and from Qarth goes by way of New Ghis.
- If Craster seems overly offended by Karl simply calling him a "bastard" in "And Now His Watch Is Ended" it's because the show does not establish it as his Berserk Button by characterizing him as the resentful Bastard Bastard of a Night's Watch ranger as the books do.
- In "Kissed By Fire", Jaime refuses milk of the poppy for his surgery without offering an explanation. In the books (and the DVD commentary) it's explained that Jaime doesn't trust Qyburn not to "beg forgiveness rather than permission" and taking his whole arm off (instead of just sealing the wound) while he's incapacitated.
- In Season 3, Robb declares Walder Frey the only lord with the reinforcements he needs despite there being no on-screen reference to the Freys being anywhere but with Robb since joining him in Season 1. By contrast, the books make the Frey withdrawal after Robb's marriage a notable event in several viewpoints.
- Moreover, in the books Robb needs Walder's allegiance because his plan is to travel North to deal with the Ironborn, rather than needing more troops.
- The Three-eyed Raven says he's been watching with "a thousand eyes and one." In the novels this has great significance as a pointed reference to the character's identity as a famous one-eyed spymaster, but in the show it's just Meaningless Meaningful Words since his identity is never explored and he has two good eyes.
- While Tormund is presumably settling his people in the Gift, Dolorous Edd and more importantly Ghost are inexplicably absent when Jon is attacked in "Mother's Mercy". The show later reveals that Ghost was locked in a kennel, but since Jon obviously resented Thorne's petulant command that he keep Ghost kenneled in "Mockingbird" and Ghost was free to save Gilly and Sam even with Jon absent just three episodes prior in "The Gift", it's still a rather questionable explanation. In the books, Edd is away serving as steward of Long Barrow and Jon locks Ghost up specifically to keep him from attacking a wildling skinchanger's boar.
- Rickard Karstark defiantly tells Robb that he will be cursed forever if he executes him in Season 3, claiming that he and Robb are kin, but it's never explained how the two men are kin, leaving some viewers to assume Rickard simply meant all Northerners are family in the symbolic sense. The books explain that Robb and Rickard are, in fact, (very) distant cousins: the Karstarks are descended from Karlon Stark who left Winterfell centuries before the Targaryan Conquest. His castle was known as "Karl's Hold" (later "Karhold") and his family "The Karhold Starks" (later just "The Karstarks"). Even in the book, however, his claims about Robb being a kin-slayer are pretty much rubbish since they're something like 10th cousins.
- In the books, Euron's personal sigil is two crows holding a crown above a slitted red eye. In the show, he uses the Greyjoys' golden kraken defaced
by a slitted red eye, even though in the books the red eye is derived from Euron's Red Right Hand, an explanation that's lost since the show Adapted Out his "crow's eye". - In the books, Robert Baratheon became king after the Rebellion because he had the strongest alternative bloodline since his grandmother Rhaelle was a sister of Aerys II's father Jaehaerys II. However, the show omits this generation, instead making Aerys II the son of Aegon V and tracing Robert's claim back 300 years to Aegon the Conqueror's bastard half-brother in a "Histories and Lore" featurette. This actually leaves the Baratheons with much less royal blood than the Martells (descendants of Princess Daenerys/Maron Martell), the Velaryons (descendants of Princess Baela/Alyn Oakenfist), and certain Penroses (descendants of Princess Eleana/Ronnel Penrose), which might not affect the succession but does make it unclear why Melisandre fixates on Stannis, Gendry, and Shireen's blood as especially "royal".
- In a more meta sense, the Adaptational Villainy of Stannis Baratheon makes it unclear why Ser Davos is in the show at all. In the books, Davos and Melisandre act as counterpart advisors to Stannis, acting as a form of Angel and Devil on his shoulders, although in a more complicated Reason and Principles vs. Pragmatism and The Needs of the Many way. With the Adaptational Villainy of Stannis AND Melisandre, and the fact that Stannis in the show doesn't particularly value Davos's input anyway, why is Davos a character? This is even worse after Stannis dies, as there appears to be no reason why any other character would care about Ser Davos or listen to his input.
- The Siege of Riverrun. In the books, both Brynden Tully and Robb's wife Queen Jeyne Westerling remained at Riverrun rather than going to the Red Wedding, and the castle never fell to the Freys, making the Siege a desperate last stand of Robb's kingdom. In the show, however, with Jeyne's show counterpart Talisa already dead and the Blackfish only having regained Riverrun from the Freys later, the motivations for the siege become a lot thinner.
- Similarly, in the books Edmure is able to negotiate the Tully garrison's surrender because he secretly allows the Blackfish to escape. In the show, however, Brynden dies fighting after Edmure orders him taken captive, meaning that the Tully garrison only go along with Edmure's order to surrender out of a somewhat forced sense that he rather than Brynden is their "rightful lord".
