Benthic microalgal communities often contribute more than 30% of the primary production of shallow coastal and estuarine areas. At Muka Head Penang (Pulau Pinang) and the Songsong Islands (Pulau Songsong), Kedah, Malaysia, high concentrations of suspended solids and phytoplankton biomass (10.6 mg Chl a m-3) has reduced water clarity such that the euphotic zone of these areas is less than 2 m and 3 m deep respectively. The benthic microalgal communities, which were composed of the diatom genera Cocconeis, Fragilaria, Paralia and Pleurosigma, had a low biomass, had low maximum quantum yields (0.325 ± 0.129), were poorly adapted to their light environment and were constantly light limited. These characteristics suggest that the benthic microalgal communities were likely to have made only a minor contribution to the total primary production of the area.