Manila Bay is one of the most significant bodies of water in the Philippines; it has abundant natural resources that have been the source of livelihood and center of socio-economic development for centuries. However, Manila Bay is affected by multiple environmental problems and challenges. These include increased organic and nutrient loading from untreated domestic, industrial, and agricultural wastes and deterioration of marine habitats threatened by anthropogenic activities. Regular water quality monitoring is ideal in these situations, however, sampling by traditional field methods would not be enough to assess the spatial and temporal variation of water quality in Manila Bay. Gathering field data for the whole bay can also be very challenging due to its extent and logistic constraints. Remote sensing fills the need for a frequent full view of Manila Bay’s water quality. This study makes use of existing bio-optical models to estimate colored dissolved organic matter (CDOM) in Manila Bay. CDOM is the mixture of organic molecules from decayed higher plants, algae, and bacteria, and is the colored portion of the total dissolved organic matter. Sentinel-3 images with concurrent field sampling on 19 July 2021 was used to calibrate and validate the bio-optical models implemented in WASI. The parameterization output showed an R² = 0.579 and RMSE of 1.274 m^−1 from lab-measured CDOM fluorescence converted to absorption. The same parameter set was used on a different image with a concurrent water quality survey on 19 May 2021 and resulted to an R² of 0.72 with the spectrofluorometer yellow substance concentrations.