Thursday's leak of a chemical used in coal processing affected about 300,000 people in the state's capital region.
Officials say it could be days before everyone is cleared to use the water.
In all, state officials believe about 7,500 gallons (28,390 litres) leaked from a Freedom Industries plant into the nearby Elk River.
The crisis shut schools and restaurants, and truckloads of water had to be brought in from out of state. People were told to use the water only to flush their toilets.
Complaints came in to West Virginia American Water about an odour and officials discovered the chemical 4-methylcyclohexane methanol was leaking out of a 40,000-gallon (151,412-litre) tank.
Federal authorities have opened an investigation.
Only 14 people exposed to the contaminated water were admitted to the hospital, and none were in serious condition. No fish kills were reported.
The chemical, even in its most concentrated form, isn't deadly. However, the compound can cause symptoms ranging from skin irritation and rashes to vomiting and diarrhea.
Company president Gary Southern said Friday that the leak had been stopped, but otherwise company officials have declined to comment.
The chemicals removed from Freedom Industries' Elk River site have been shipped to another facility that the company owns, said Jimmy Gianato, state Department of Homeland Security director. The facility is in nearby Nitro, not near a water source.