An anti-pollution official said the Mehdiganj plant in Varanasi in the state of Uttar Pradesh had breached the conditions of its operating licence, prompting the closure order earlier this month.
"The plant is closed following our orders," Uttar Pradesh Pollution Control Board secretary J.S. Yadav said on Wednesday.
"They have also been asked to take suitable measures to recharge the depleting groundwater level by twice the amount they have extracted.
"Also, the effluents released by the plant contain pollutants beyond the permissible limits."
The company has appealed against the closure order to India's environment court, the National Green Tribunal, saying the allegations are false.
Hindustan Coca-Cola Beverages, a unit of Coca-Cola, said the plant had been "complying with all regulatory approvals and applicable laws" for 15 years.
The unit said in a statement that it was confident the courts would find that it had acted in the "best interests of the communities we serve".
The company hit a hurdle earlier this year when local authorities said they would demolish the Varanasi plant, claiming it was built on village council land and was "illegal".
The authorities also imposed a 126,000 rupee (HK$16,380) fine on the company over the issue.
Protests have been held against Coke's bottling plants in other parts of the country, alleging depletion of groundwater and pollution.
Activists welcomed the Varanasi plant's closure, claiming the company had a dismal environmental record.
"Coca-Cola's thirst for profits in India has placed its business interests over the well-being of communities and the environment and this is not acceptable," said Amit Srivastava of activist group India Resource Centre.