Those breakdowns happened on June 3 near the Mission Bell Truck entrance, and again on June 10 along Granada Drive.
During a council meeting on Wednesday, city leaders said a new 42-inch pipe will be installed at the Nutrien Site.
Crews are using a slide rail system to protect the water main and prevent risks of caving in.
The estimated costs of the work is $1.5 million.
The city of Madera is now working to adopt a resolution for emergency response and repairs for the sewer.