While Audrey and Agent Howard are pulling the books out to access an escape hatch in the Stateroom.
Agent Howard: "We're dealing with killers and terrorists in the real world while you're out here holding hands with the children of the corn." (referencing a Stephen King story)
Audrey: "At least I'm not like that one guy you trained that was chasing aliens...what was his name?"
Howard: "Hey, he was a genius. What happened to him the last few years was a tragedy, but that's beside the point." This is a reference to Fox Mulder and the 2008 movie (a "few years" before Haven aired, as Howard states) The X Files: I Want to Believe (2008).
On at least two occasions Little Tall Island is mentioned. This island does not exist, but Stephen King's "The Storm of the Century" takes place on Little Tall Island.
Opening scene poker game, Ezra asks Audrey her favorite nut and lists as examples "cashews, almonds, pecans, walnuts, macadamias." Audrey answers "pistachios." Ezra says "Technically not a nut; it's actually a seed" and goes on about it being a culinary nut but a botanical seed. Cashews, almonds, pecans, and walnuts are also botanical seeds and not nuts.
Duke's ship, the Cape Rouge, really did sink in the LeHave River in 2014.
In the metal room where Audrey and her FBI boss are locked in on Duke's boat, Audrey pulls out the first drawer below a table. A ukulele is in front obscures it as a bookshelf. In the middle of that bookshelf is a copy of Stephen King's "The Tommyknockers" which takes place in a town named, ohhhh Haven, Maine.