A milk factory owned by Sameer Agriculture and Livestock Limited has been shut down indefinitely for failure to comply with waste disposal regulations.
The production manager at the Daima plant in Industrial Area, Mr Kenneth Kareithii, was also arrested in the Tuesday morning raid by police and inspectors from the National Environment Management Authority (Nema).
Nema accused the factory of discharging effluent into Nairobi River.
The Authority's acting director general Mamo B. Mamo said they would crackdown on factories along the river that have flouted effluent regulations.
"Nema has identified 102 discharge points along Nairobi River. Out of inspections conducted, 50 percent of firms have complied. Ongoing inspections is to ensure remaining have complied as per Water Quality Regulation 2006 or be shut down and (officials) prosecuted," Mr Mamo said.
Nema officials also raided Synresins chemical factory that manufactures resins used in paints, inks and textiles and arrested its CEO Mira Shah, production manager Michael Mungai and human resource boss Yvonne Nyokabi.
Mr Mamo also closed down the factory saying it was discharging hazardous waste direct into the sewer and the environment.
On Monday, Nema shut down Modern Lithographic (K) Ltd, Apex Limited that manufactures paints, Thorlite Kenya Ltd and Kamongo Paper Recycling Company, all in Industrial Area.
So far the environment watchdog has raided 53 facilities.
The crackdown follows an exposé by Nation on pollution of Nairobi River that revealed that the it was suffocating with a cocktail of raw, untreated sewage from everywhere, including some lavish estates in the city.
The two-month river pollution investigative project, dubbed “#ToxicFlow”, trailed the river from Kiambu County where it starts, through Nairobi, Machakos, Makueni, Taita Taveta and Kilifi counties, until it exited into the Indian Ocean at Sabaki Bridge.
Nema says it is not its responsibility to clean the river but that of the county government. It says its role is to ensure that companies comply with environmental regulations.
Those arrested in the raids will be arraigned Wednesday.