Agreement in "[Singular Noun / NP] + Is/Are + [Plural Noun / NP]"?

1. My fish's native habitat is rice fields.

2. My fish's native habitat are rice fields.

Which one is correct? I'm pretty sure it's the first, since 'is' modifies 'habitat,' but it still sounds weird...

It may sound weird, but it is still correct. Singular nouns take singular verbs. In this case, the singular noun is habitat. Thus, is is the correct form of the verb to be in this case.

My fish's native habitat is rice fields.

To make it sound more natural, you could reverse the order thus:

Rice fields are my fish's native habitat.