The study identifies the relative contribution of various bio-optical factors to the total attenuation of ultraviolet radiation (UVR) wavelengths and photosynthetically active radiation (PAR) in temperate coastal waters of Japan by surveying the physical properties of the water column, UVR and PAR penetration, and the absorption characteristics of dissolved and particulate material. Spectral absorbance properties of pigment (a_ph), detritus (a_d) and chromophoric dissolved organic material (a_CDOM) displayed both seasonal and wavelength specific variability. On an annual basis, absorbance by a_CDOM was the highest absorbing fraction (47–59%) for the UVR wavelengths measured (305, 320, 340 and 380 nm) but decreased (32%) at 450 nm. Contribution of pigments to total absorbance was highest (40–60%) during a spring bloom for both UVR and PAR. A large variability (C.V. > 42%) for annual average attenuation coefficients (K_d[λ]) at respective wavelengths observed suggests that the spectral composition of the water column changes throughout the year in this region. A significant relationship was observed between K_d(λ) and a_CDOM at 305, 320, 340 and 380 nm only (P < 0.01) but not for 450 nm (PAR) indicating the role of CDOM in regulating variations in K_d(λ), particularly in the UVR range. The slope S, obtained from a natural-log plot of the absorption coefficient of CDOM against wavelength, ranged between 0.014 and 0.036 nm⁻¹ annually (average = 0.020±0.007, C.V. = 35%) and suggests seasonal changes in the origin of CDOM between terrestrial (low S) and biogenous (high S) CDOM.