Surface water samples collected during the monsoon and inter-monsoon seasons of 2009 off the east coast of Peninsular Malaysia have been analysed for concentrations of total chlorophyll, suspended particulates and coloured dissolved organic matter (CDOM). Spectral absorption coefficients of dissolved and particulate materials have also been measured. Significant seasonal variabilities in concentrations and optical properties were reported with high concentrations of all parameters during the northeast monsoon (NEM) season and low during the southwest monsoon (SWM) and inter-monsoon seasons. Contrary to previous reports on the oligotrophic nature of the waters during the inter-monsoon season, relatively high concentrations of chlorophyll (>3 mg m−3) were observed at offshore stations in the study area in the spring and fall inter-monsoon months. The chlorophyll-specific absorption spectrum changes with the seasons with the greatest absorption per unit chlorophyll during the SWM and the least during the inter-monsoon seasons, probably in response to seasonal changes in phytoplankton community and cell size structure. The water is classified as optical case 2. At the blue end of the spectrum (440 nm), light absorption by non-phytoplankton materials (CDOM and detritus) accounts for nearly 70% of the total non-water absorption regardless of the season. At the wavelength (676 nm) of the secondary chlorophyll absorption peak in the red part of the spectrum, light absorption by chlorophyll contributes 80–90% to total non-water absorption at most stations and this may provide the basis for remote sensing of phytoplankton chlorophyll in these waters.