The plumbing system at Rikers Island is being tested after two inmates were diagnosed with Legionnaires' disease in the last year.
One of those inmates is still hospitalized.
Multiple showerheads have already been cleaned and removed as a precaution.
The department of correction says the inmates can still use the water, but inmates at higher risk for the disease are being forced to use showers that have been treated.
"The health and safety of our officers and the people in our custody is our top priority. We are working closely with the Health Department and implementing all safeguards," the Department said in a statement.