You're right about "naturally" and "elements", but "occurring" is actually a verb participle that is modifying "elements". So we have the noun phrase: "naturally occurring elements".
It's usually adjectives that modify nouns, but sometimes verbs can do that too, for example:
A sleeping child. The condemned man. The gleaming showroom.
In those examples, the verbs "sleeping" and "gleaming" are present participles, and "condemned" is a past participle. They are not actually adjectives as such, but they are all modifying nouns, just like 'real' adjectives would do.
Yes, the adverb "naturally" modifies "occurring". As a noun modifier, we call "naturally occurring" a VP (verb phrase. Here are some more VPs comprising adverb-verb combinations:
A recently discovered fossil. His recently published article. The rapidly melting ice cream.