Dr Muia said that water bowsers not registered with the county will be banned.
The county will also start sensitising residents about healthy behaviours such as drinking boiled water.
The Nairobi County government has started a crackdown on eateries without valid licences and unregistered water vendors, amid a cholera outbreak.
Speaking to the Nation on Sunday, Dr Bernard Muia, the county's Health executive, said he had directed public health officers to rein in eating joints that do not have valid food handling certificates, in an effort to contain the spread of the disease.
"I have instructed public health officers to ensure that eateries without licences and are being operated without even a toilet be given 24 hours to conform to the provisions of the Health Act or risk being closed down, and owners arrested and arraigned in court," Dr Muia said.
Dr Muia also said that water bowsers not registered with the county or the Nairobi City Water and Sewerage Company will be banned.
Additionally, public health officers will randomly inspect water supplied to the residents to determine whether it is fit for consumption.
"Our health officers are now going round the city looking at the water tankers to validate whether they are registered and also to know the status of such water being supplied," he said.