The correct choice is indeed A, although my road to Rome is different.
Let’s look at the grammar first.
After increasing steadily for centuries, the total annual catch of all wild fish peaked in 1989; since that time,
the total catch for most species has declined or plateaued, prompting conservation efforts designed to help prevent population crashes and possible extinctions.
A. fish peaked in 1989; since that time, the total catch for most species has declined or plateaued, prompting—
1. The total annual catch of all wild fish peaked in 1989; this is IC 1 with a sub and verb of its own.
2. Since that time- means from that time or after that time, since is a preposition here and not a subordinate conjunction.
3. Since that time, the total catch for most species has declined or plateaued—this is IC 2, with a subject and verb of its own. Ignore for the time being, - since that time – which is an introductory prepositional phrase.
4. prompting conservation efforts designed to help prevent population crashes and possible extinctions – A modifier with a present participle( prompting) and a past participle( designed); Ask the question what prompted the conservations efforts? You will get the answer as the act of declining or the plateuing.
A perfectly grammatical structure.
B. fish peaked in 1989, but with the total catch since then declining or plateauing in the case of most species, prompting ---
The IC 1 is ok, but the second IC is lacking a working verb; therefore, the structure is a fragment. C. fish had peaked in 1989; since that time, the decline or plateau of the total catch for most species, which prompted --
importantly, the second IC lacks a working verb for the subject decline or plateau. ''Prompted is the verb of the relative clause that starts with which. So the second part is again a fragment.
D. fish, which peaked in 1989, and, in the case of most species, it has declined or plateaued since, prompted ---
bunch of errors here. Structurally, the relative pronoun which refers to fish, while it should refer to the catch, because it is the catch that peaked, and declined or plateaued. Secondly, the pronoun ‘it’ is redundant. Thirdly the part - which peaked in 1989, and, in the case of most species, it has declined or plateaued since – is unparallel; fourthly, the choice says the catch of the wild fish prompted the conservation measures, which is factually incorrect( after ignoring the portion that is offset in commas) E. fish, which peaked in 1989 but has since declined or plateaued for most species, and this prompted --- The same problem of touch rule of relative pronoun which as in D; Serious error in meaning since the choice means to say that the catch of the wild fish prompted conservation efforts. It is actually the decline or the flattening the prompted the conservation efforts.
So one may see the simpleness and correctness of A. All in all, a comprehensive wholesome question to practice modification, relative pronoun touch rule, meaning change, redundancy,and fragmentation - OMG! what is left! a kudo to the poster.