The development of an operational water quality monitoring method based on remote sensing data requires information on the apparent and inherent optical properties of water (AOP and IOP respectively). This study was performed to determine the apparent and inherent optical properties of coastal waters of the Mahakam Delta, Kalimantan, Indonesia. Inherent optical properties (IOPs) were derived from above-water radiometric measurements and ocean color model inversion. Retrieved IOPs and measured concentrations show good agreement both for total suspended matter (TSM) and chlorophyll a (Chl a) (R2 = 0.72 and 0.80 respectively). The linear relationship between the retrieved IOPs and the measured concentrations was then used to estimate the specific inherent optical properties (SIOPs) using the basic equation of the Lambert–Beer law. The specific backscattering coefficient of TSM (View the MathML source) was found to be 0.0087 m2 g−1, and the specific absorption coefficient of Chl a (View the MathML source) was found to be 0.023 m2 g−1 in the Mahakam Delta. The estimated values of SIOP for TSM and Chl a could be considered spatially constant for the Mahakam Delta, and resulted in reliable estimates of TSM and Chl a concentrations (R2 = 0.84 and 0.85 respectively). The specific backscattering coefficient of TSM found in this study is similar to that of the Barito Estuary (in the southern part of Kalimantan) but lower than that of the Berau Estuary (in the northern part of Kalimantan), whereas the specific backscattering coefficient of Chl a is similar to that found in the Berau Estuary. This study contributes to the development of an operational method based on remote sensing data to map water constituent concentrations in the Mahakam Delta, as well as to enrich the information about the optical properties of Indonesian waters.