Seasonal changes in the assemblage structure of dominant epipelic diatoms were studied along a transect crossing a salt marsh, sandflat, and mudflat of an estuarine intertidal shore at Berrow Flats, Somerset, UK. Seasonal changes in cell numbers displayed different patterns in the salt marsh and sandflat/mudflat. At salt marsh sites highest numbers of individuals were recorded in summer followed by a smaller autumn growth, while in the sandflat lower numbers showed no seasonal pattern. Repeated annual patterns in the succession of taxa were not observed as environmental conditions changed at the study site with time. Measurements of salinity, pH, interstitial water content, air and soil temperature were taken together with the diatom samples. A canonical correspondence analysis was employed to relate seasonal changes in assemblage structure to measured environmental variables. Total percentage variation in the first four axes of the species/site-environmental biplots ranged between 54 and 66°. In winter, sites and species separated most significantly along gradients of salinity and levels of organic matter. In spring and autumn, interstitial water content became a more significant environmental variable. By summer steep gradients in pH, levels of organic matter, and hypersaline conditions separated sites and assemblages into more discrete groups when compared to the more even spread of points in the other seasons. The results indicate that different combinations of environmental variables influence diatom assemblage structure seasonally.