Treated waste flows from the Morgantown, W.Va., wastewater treatment plant into the Monongahela River. The plant receives effluent from a Mylan pharmaceutical factory.

A cacophony of machines, some as big as a dump truck, mix pharmaceutical ingredients, press them into tablets, and fill capsules at a West Virginia factory owned by generic-drug giant Mylan. By the end of each run, the walls, ceilings, floors, and nearly every nook and cranny of the intricate equipment were caked in powdery drug residues, say three former Mylan employees.

No matter how much the machines and floors were swept and vacuumed and wiped down, “there was always powder left on the machines and walls,” said one employee who worked in packaging and other manufacturing roles for nearly five years until being laid off last year. “You see the powder everywhere.”