The flushing process was detailed Wednesday by Lake Jackson City Manager Modesto Mundo, who noted the flushing process and existing boil advisory are separate issues from the recent tests that showed the presence of a deadly amoeba.
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A boil order remains in place for the city after tests showed the supply had low disinfectant levels.
A now-expired Do-Not-Use advisory from the Texas Commission on Environmental Quality was related to the discovery of a microbe known as a brain-eating amoeba.
"They need the water to hit a chlorine threshold level of 1.0 and then they have to maintain that for 60 days," Mundo said. "That 60-day period has not started yet."
Results from water samples taken over the weekend showed chlorine levels were not up to standards, according to Mundo.
Crews continue to flush the system and the process is putting a strain on the city's reliance on water wells. Lake Jackson shut off its supply from Brazosport Water Authority, which accounted for half its water source.
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"We want to make sure we can maintain that well capacity," Mundo said. "We need to lower our usage."
The boil notice could last as long as two to three weeks.
Mundo's briefing came a day after Texas Gov. Greg Abbott visited the city and three days after a disaster was declared for Brazoria County.
READ THE FULL DISASTER DECLARATION ON THE GOVERNOR'S WEBSITE
Lake Jackson's water crisis began with the discovery of Naegleria fowleri, an amoeba that typically affects people when contaminated water enters their body through their nose, according to the CDC.
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It can travel to the brain and cause a condition known as amebic meningoencephalitis, a rare but highly lethal disease, according to health experts.
The CDC said people cannot get infected from swallowing water contaminated with Naegleria fowleri.
SEE ALSO: 6-year-old Lake Jackson boy dies suddenly of brain-eating amoeba
As the city navigates the crisis, crews are being sent out to homes and businesses to look for any breaches to the system. The personnel may ask homeowners for permission to inspect areas outside of homes and will have proper identification, Mundo said.