The National Environmental Management Authority (Nema) will close down 25 factories accused of discharging effluent into Nairobi River.
The authority in a joint effort with the Nairobi County said three factories would be shut down on Wednesday.
Giloil Industries was the first to be shutdown leaving workers at the cooking oil maker stranded.
The plant is accused of failing to comply with regulation regarding effluent discharge.
Nema says it has already shut 15 other factories for non-compliance.