Honolulu will pay a $100,000 fine and update its storm water and sewage spill procedures under an agreement reached with the state Department of Health.

The consent agreement stems from an August 2015 spill that closed Waikiki Beach for two days. At the time, the city blamed the overflows on miscommunication with a contractor who was upgrading a pump at Ala Moana.

In an agreement reached with the state health department Friday, health officials say the discharges violated state laws limiting water pollution.

“The size of the spill was affected by city personnel inadvertently turning off the high level alarms at the Ala Moana Pump Station, which are set to warn city personnel of potential spill conditions,” the order says.

The city Department of Environmental Services said Friday that it has agreed to the order, which resolves the agency’s liability for the incident and doesn’t involve any admission of fault.

The order requires the city to revise how it estimates sewage spill volumes and improve how it responds to spill prevention alarms.

The city will also upgrade its program for managing the sewer system, known as the “sewage system supervisory control and data acquisition system,” and develop a study of how storm water impacts high-density urban areas.

The city must additionally pay the state $100,000 within 90 days.

The storm that took place on Aug. 24, 2015 resulted in nearly 5,000 gallons of sewage and stormwater discharged at the Kaneohe Pretreatment Facility; about 125,000 gallons spilled at the Kailua Regional Wastewater Treatment Plant, and more than 462,000 gallons spilled in Kakaako and Ala Moana.

The city is already under a separate $5.2 billion consent decree with the U.S. Environmental Protection Agency to upgrade its wastewater system. Honolulu Mayor Kirk Caldwell is seeking $655.9 million for sewer upgrades in his budget request this year.