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.
Option Elimination -
(A) an increase in their use can create serious environmental problems such as water pollution, and their substitution for more traditional fertilizers - We are looking for a contrast after "whereas," and this option communicates the contrast clearly. "whereas the use...", an increase in their use ...can cause ....and an increase in their substitution...may accelerate....ok.
(B) an increase in their use can create serious environmental problems like water pollution, and if substituted for more traditional fertilizers, it - for example, we need such as and not like. Wrong.
(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 - used increasingly? Or increasingly used. "substitutions"? Moreover, the structure is a bit confusing. When we have a contract in the beginning, then directly talk about why to add one more conditional with "if."
(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 - We need "and" as while makes no sense. We have a contrast and, again, contrast. The bigger problem here is the "comma" after the "while phrase." Because of that comma, we essentially have an "independent clause" comma " independent clause" which is wrong. To make it a correct construction, we don't need a comma after "while phrase here." E.g., She studied diligently for the exam while her friends went out to the movies.
(E) the increased usage of these fertilizers can create serious environmental problems like water pollution, while their substitution for more traditional fertilizers - for example, we need such as and not like. Wrong.