The season covered about 1/4 of the book, the next season is expected to cover about the same (1/4), making it 2/4 of the third book. Some events that take place in the series are nowhere to be seen in the book, and some events are dragged forth from the fourth book (A Feast For Crows).
There is no Theon Greyjoy in the third book (The Storm of Swords) (he is only mentioned once, at the Red Wedding).
Some battles which should have taken place at this timeline in the book are missing from the series.
A lot of Arya, Jon, Bran, Sansa, Tyrion, Davos chapters/events are not shown in the series.
Osha and Rickon are not traveling with Bran and the rest of his party.
A character named Coldhands is missing from the series (mayhaps they will include him in the next season).
Davos doesn't teach himself how to read, he is thought by a Maester.
Davos actually saves another Roberts bastard and not Arrya's friend.
When Sam and Gilly are attacked in the village while fleeing from Craster's Keep, Sam doesn't actually kill an Other but a wight (a brother of the Night's Watch he used to know called Small Paul), it is here that he gets saved by the character Coldhands.
The Red Wedding is more brutal, and there are a lot differences around it, also Arya doesn't see the direwolf get killed, and The Hound fights some men of and lands an axe on Arya's head to prevent her from running to her death.
These are some differences, there are many more. It's really a clash of book chapters and series episodes. The series is just a jumble and a tease to the fans, it doesn't get into the core things happening in Westeros, a lot of the events around history of the characters are lost or thrown out, only key events are kept and even they are crippled.
As far as chapters are concerned, there is no chapter per episode or even several chapters per episode kind of thing, it's more of an events per episode kind of thing. And since some event have been omitted and some randomly thrown in, it is kind of hard to point at a chapter and tell exactly where it is in the series, it's more of a jumble of events. I can tell you from rereading the book that the first two or three episodes of the series roughly take the events and chapters from the first 400 pages of the book and jumble them up in those three episodes. Then they suddenly jump ahead to the events of 700-800 pages, and take it from there, but omit some events which will probably be in the next season.