New bacteria is growing in the plant and does treat some of the sewage, but that bacteria is still up to desirable levels, Thomas said.
The chemicals toluene and xylene, which are common in plastics, insecticides, paint and many other manufacturing products, were the contaminants that killed the bacteria and prompted the shutdown, Thomas said Tuesday.
Although the chemicals have been identified, it was not known Tuesday who put the chemicals into the sewer system and how much of the chemicals made their way to the city plant.
"It narrowed it down to a zillion" possible culprits, he said.
The chemicals could have been dumped by a business or "someone trucking it in and dumping it in manholes," he said.
Thomas said it was highly unlikely the chemicals came from a residence because it would take a large amount of the chemicals to affect the plant as they did.
Plant Superintendent Donald Barton said Monday those chemicals could have come from bacteria-rich sludge hauled from Washington County sewer plants to the city plant in an effort to grow new bacteria for treatment.
But Barton and Thomas said Tuesday that further analysis showed the concentrations of the chemicals was too high to have come from the county sludge.
Thomas said the chemicals also have been found at a county sewer plant, so there is the chance that some of the chemicals were dumped into the county system.
When the plant was shut down Saturday, the high-purity oxygen used in the treatment process was turned off. The city uses the oxygen to help the sewage-eating bacteria thrive and to make the ozone used to disinfect the waste water.
The phases of the treatment process that filter out large material and sludge continued as normal while other parts of the treatment process were stopped.
Without ozone to disinfect the waste water, high levels of fecal coliform bacteria flowed into the creek. Fecal coliform bacteria come from feces and can cause infections.
At about 1 p.m. Tuesday, the Hagerstown plant switched to using chlorine to disinfect the waste water as it left the plant.
McIntire said the chlorine will effectively kill the fecal coliform.
The public has been advised not to come into contact with the creek.
MDE officials inspected wildlife on the creek Monday and Tuesday and found no ill effects from the contaminated waste water.
McIntire and Washington County Health officials have said the polluted waste water should pose no risk to drinking water since any contaminants would be diluted by the creek and later the Potomac River.
McIntire said the MDE will continue to monitor the creek.