The spatial variation of microphytobenthos was investigated with reference to both the estuarine gradient and the intertidal levels of the Gironde estuary, France. Four transects, each with three stations, were surveyed in two different seasons (April and October) during two consecutive years. In addition, the seasonality of microphytobenthic pigment concentration and its relationship to environmental factors were examined by means of weekly sampling at an intertidal mudflat located in the oligo-mesohaline area. Generally, microphytobenthic pigments increased both with increasing salinity and tidal height. Clear seasonal variations were found for microphytobenthic chlorophyll-a concentration. Multivariate analysis showed environmental factors such as temperature, insolation, salinity and sand content of sediment to be most determinant in explaining these variations, with different sets of factors controlling the variables at each station. The principal explanatory factors with regard to chlorophyll-a concentration at both stations were variables known to be related to primary production, such as temperature (52%) at the lower intertidal station, and insolation (9%) and salinity (29%) at the higher intertidal station. The restricted primary production in the water column, due to the high turbidity of the Gironde estuarine water and the proportional area covered by intertidal areas, underlines the importance of the microphytobenthic biomass, and probably production, for the estuarine ecosystem.