<p>Remote sensing of coral reefs requires accurate parameterization of water optical properties to filter upper-layer water effects in surface reflectance signals. This study analyzes bio-optical and biogeochemical characteristics in coral reef waters of the South China Sea, focusing on three geomorphological zones: Lagoon, Fore Reef, and Fringing Reef. Significant spatial variability is observed across these zones, influenced by nutrient inputs and hydrodynamic mixing. Fringing Reef waters, affected by land-based nutrients and coastal advection, exhibit high variability in optical parameters, with chlorophyll-a concentrations averaging around 1.66 ± 1.47&#xa0;μg&#xa0;L⁻¹—approximately tenfold higher than those in Lagoon and Fore Reef zones. Strong mixing in Fore Reef and Fringing Reef zones results in elevated suspended particulate matter (SPM), with inorganic particles constituting a large proportion (0.75 ± 0.05 and 0.68 ± 0.26, respectively). Lagoon waters have a more balanced composition, with an inorganic-to-total particulate ratio of 0.52 ± 0.28. Nearshore Fringing Reef waters show a complex particulate composition, with both phytoplankton and non-algal particles contributing nearly 50% to absorption. Across all zones, colored dissolved organic matter (CDOM) dominates UV absorption, with absorption coefficients 3–10 times higher than those of particulate matter. We established an accurate chlorophyll-a concentration model from <i>a</i>_<i>ph</i>(440) (<i>R</i>² = 0.93, RMSD = 0.34&#xa0;μg/L⁻¹). Additionally, <i>a</i>_NAP(440) demonstrates significant correlation with turbidity (<i>R</i>² = 0.84), highlighting its potential as an optical proxy for turbidity, offering value for remotely sensed monitoring of coral reef water quality. These insights enhance our understanding of bio-optical variability in coral reef waters and supports improved remote sensing applications for coral reef monitoring.</p>