Chemists and medical technologists of the Environmental Management Bureau-National Capital Region conduct water testing samples taken from different parts of Manila Bay and the three major river systems of Metro Manila.

The water samples are tested for the presence of, among others, heavy metals, nutrients, and fecal coliform to determine its conformity with set water quality standards for both Class SB (Marine Waters) and Class C (Freshwater). In 2019, DENR inspected several business establishments near the Manila Bay. Water quality monitoring conducted by the EMB-NCR revealed that some restaurants and other business establishments released and leaked massive amounts of wastewater into the bay. 

With the bay facing several problems arising from the improper use of its resources that caused the continued decline in the water quality and the quick deterioration of marine habitats that can be found in the area, the Supreme Court of the Philippines, in its ruling (G.R. 171947-48) dated 18 December 2016, has ordered DENR and 12 other government agencies to clean up, rehabilitate, and preserve Manila Bay, and restore and maintain its waters to SB level to make its waters fit for swimming, skin-diving and other forms of contact recreation.

The EMB National Capital Region under the leadership of Regional Director Domingo Clemente, Jr. has been busy doing water quality sampling and monitoring during MECQ and GCQ in Metro Manila—whilst observing stringent health safety protocol.