Over the next few years, increasing demands on the Chattahoochee River, which flows into the Apalachicola River, could alter the saline content of Apalachicola Bay, which would rob the oysters there of their flavor, and to make them decrease in size, less distinctive, and less in demand.

Complete question:

Over the next few years, increasing demands on the Chattahoochee River, which flows into the Apalachicola River, could alter the saline content of Apalachicola Bay, which would rob the oysters there of their flavor, and to make them decrease in size, less distinctive, and less in demand.

(A) which would rob the oysters there of their flavor, and to make them decrease in size,

(B) and it would rob the oysters there of their flavor, make them smaller,

(C) and rob the oysters there of their flavor, making them decrease in size,

(D) robbing the oysters there of their flavor and making them smaller,

(E) robbing the oysters there of their flavor, and making them decrease in size

Robbing the oysters there of their flavor and making them smaller

Explanation:

“Robbing the oysters there of their flavor” is now an improvement, providing us more details about the entire previous paragraph on increasing demand for either the river and improvements in saline quality.  

This is perfectly reasonable: the whole long-running situation–starting with the "increasing demands" on the river–robs of its flavor oysters, so that the "ing" changeover is fine.

At the end of the sentence, too, there is a perfect comparison: "making them bigger, less conspicuous and less requested." Three parallel modificators, both explaining what's going on with the oysters.