Inshore estuarine, lagoonal, and reef waters of the Great Barrier Reef (Australia) were sampled between 2002 and 2005 during four dry and one wet tropical seasons. Relationships among three biogeochemical concentrations and five key water optical parameters measured at 129 stations were explored to optically characterize six predefined regions. A significant spatial and seasonal variability in some of the inherent optical properties and concentrations measured was found, reaching over two orders of magnitude in the estuaries. Total suspended solids concentrations ranged from 0.5 to ∼54 mg L−1, TChl‐a ranged from 0.05 to ∼9 mg m−3, color dissolved organic matter (CDOM) ranged from 0.004 to 0.8 m−1 at 440 nm, and the backscattering coefficient ranged from 0.001 to 1.18 m−1 at 555 nm. Our data set was mainly composed of coastal stations (95%), leading to a poor correlation between the three concentrations (R2 < 0.31). The range of variation in backscattering ratios, power law exponents, and the spectral slopes of CDOM and nonalgal particulate matter is comparable with findings from other coastal and open waters around the world. The empirical relationships between TChl‐a and aph(440) were found to differ from reference models, indicating differences in phytoplankton size structure and populations. High variability in backscattering ratios and associated power law exponents as well as particulate absorption ratios indicated different trends or relationships in particle size and composition between the different regions. Stations close to the reef matrix showed specific characteristics with concentrations typical of oceanic waters but CDOM spectral slopes similar to those of coastal environments.