Whereas the use of synthetic fertilizers has greatly expanded agricultural productivity in many parts of the world,
an increase in their use can create serious environmental problems such as water pollution, and their substitution for more traditional fertilizers may accelerate soil structure deterioration and soil erosion.
The structure is Whereas X, Y -> X and Y should be parallel and should be clauses.
(A) an increase in their use can create serious environmental problems such as water pollution, and their substitution for more traditional fertilizers -> Looks good. this option is parallel -> whereas the use of X, an increases in their use of Y
(B) an increase in their use can create serious environmental problems
like water pollution, and if substituted for more traditional fertilizers,
it (C) if these fertilizers are used increasingly, they can create serious environmental problems such as water pollution, and if used as substitutions for more traditional fertilizers, they
if used as substitutions for more traditional fertilizers -> what is used?
The subject of the sentence is ellipsed. So we can repeat that subject as
if these fertilizers are used increasingly, they do X, and if these fertilizers are used as substitutions for more traditional fertilizers, they do Y .
Instead of that, we can use "and if these fertilizers are substituted for more traditional fertilizers, they do Y" -> We can eliminate this option based on redundancy. (D) the increased usage of these fertilizers can create serious environmental problems such as water pollution, while if substituted for more traditional fertilizers,
this substitution
while is used as but for contrast.
what is substituted?
Since we have a "while", we can repeat the subject which is "the increased usage of these fertilizers substituted for more traditional Fertilizers" -> Wrong sense.
this is pronoun and cannot refer to the clause. (E) the increased usage of these fertilizers can create serious environmental problems
like water pollution, while their substitution for more traditional fertilizers