The abundance and distribution of microphytobenthic pigments determined by HPLC (chlorophylls and carotenoids) were compared between muddy and sandy sediments of the Tagus estuary (Portugal). In the two types of sediment, with similar periods of illuminated emersion, chlorophyll a concentrations on a per area basis (mg m(-2)) were comparable (down to 2 mm). Pigment analysis also revealed similar microphytobenthic communities in terms of algal classes. Diatoms were the dominant microalgae, but cyanophytes, euglenophytes and phanerogam debris were also present. For both muddy and sandy sediments, microphytobenthic biomass showed a high level of variability both within and between two consecutive years. Microphytobenthos was highly stratified in the mud, with most of the chlorophyll a occurring in the top 500 pm. In the sand, relatively constant concentrations were found throughout the sediment profile down to 3 rum. This is probably related to deeper light penetration in sandy sediment and/or increased physical mixing caused by invertebrate activity or overlying currents, leading to the burial of an important fraction of the microphytobenthic cells. Differences observed in the intensity of sediment coloration of muddy and sandy sediments might have resulted from the different vertical distribution of benthic biomass. (c) 2005 Elsevier Ltd. All riahts reserved.