Manila Bay is one of the most significant harbors in the region, enabling commerce and trade between the Philippines and other countries. Its abundant natural resources have provided for generations of its inhabitants and have driven socio-economic development for centuries. Like other water bodies adjacent to highly urbanized cities, the increased organic and nutrient loading from untreated domestic, industrial, and agricultural wastes resulted to further degradation of its water quality. While frequent water quality monitoring is ideal, data from traditional field sampling methods might not be sufficient to assess the spatial and temporal variations of water quality in Manila Bay. Remote sensing fills the need for a frequent and full overview of the bay’s water quality. Sentinel-3 images were initially processed through the Case 2 Regional CoastColour (C2RCC) model to retrieve the remote sensing reflectance. The Normalized Difference Chlorophyll Index (NDCI) was computed for the images and were modeled against the C2RCC-derived chlorophyll-a estimates. From this, we were able to get a general equation (TNDCI – transformed NDCI) to retrieve chlorophyll-a concentrations from two reflectance bands (Oa8 and Oa11). TNDCI gave an R² of 0.9 and RMSE = 5.12 µg/L as compared to C2RCC values, and an R² = 0.85 and RMSE = 2.44 µg/L with field data.