Indonesia has almost 8,000 watersheds, and 5,700 rivers, divided into over 131 river basins. Three key institutes help monitor and manage water quality in Indonesia. The Ministry of Environment and Forestry monitors water quality and pollution control and reports findings annually. River basin organizations also assist in conducting sampling, laboratory measurement of water samples, and water patrol. Lastly, the Ministry of Health is tasked with the protection and improvement of public health, regulation of drinking water standards, and monitoring of drinking water quality provided by water supply agencies (Asian Development Bank, 2016).

The government is responsible for setting water quality targets for individual water systems and rivers. The targets can be changed every year if the water quality has improved. Some local governments choose to set more strict effluent targets for industrial discharges into water resources within their jurisdiction. In Indonesia, water quality is classified into four groups. Class I is the water that can be used as standard water for drinking purposes; Class II is the water used for water recreation, fresh fish preservation, livestock, water for irrigation, and other usages requiring the similar quality; Class III is water that is used for machinery or at facilities of fresh fish preservation, livestock, water for irrigation, and/or other usages requiring the similar quality; and finally, Class IV is water that is used solely for irrigation, and other usages requiring similar quality (Asian Development Bank, 2016).