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Hermione always liked to go through their exam papers afterward, but Ron said this made him feel ill, so they wandered down to the lake and flopped under a tree. The Weasley twins and Lee Jordan were tickling the tentacles of a giant squid, which was basking in the warm shallows. (Harry Potter and the Sorcerer's Stone)

Though the head of noun phrase before 'which' is tentacles, 'which' seems to refer to squid, because of the singular verb ‘was’. Can 'which' refer to the closest noun before it, not the head?

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    Note however that squid is the head of the NP a giant squid (unless you hold, as some radicals do, that NPs are headed by determiners).
    – StoneyB on hiatus
    Commented Aug 6, 2013 at 10:21

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Yes, it can refer to the closest noun too, as in the following sentence.

All I can say is that I finally picked up Gima's cookbook last spring at the age of 41, when I found it at the bottom of a box, which I was finally unpacking because I was finally settling into the house where I hope and pray to finally stay put.

It is the box being unpacked, not the bottom of the box.

It depends on the context, though. In the following sentence, which is not referring to crime but to "he has never been convicted of a crime."

He has never been convicted of a crime, which suggests that he doesn't pose a threat to society, legal experts said.

It's not a crime that suggests he doesn't pose a threat to society, but the fact he has never been convicted of a crime.

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    +1 The second part takes this answer to a higher level of usefulness.
    – StoneyB on hiatus
    Commented Aug 6, 2013 at 10:49
  • @stoneyB, I suspect when the head of NP and which don't match, they put comma. For when there isn't it, they would think which is naturally refer to the head. Is this not proper idea?
    – Listenever
    Commented Aug 6, 2013 at 13:20
  • @Listenever The comma before which is normally used because which introduces a nonrestrictive clause. The NOAD says: "A nonrestrictive clause is set off within commas, and which, who, or whom, not that, is the relative pronoun to use as the subject or object of the verb of the clause."
    – avpaderno
    Commented Aug 6, 2013 at 17:21

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