Epilithic diatom communities of the Clyde Estuary demonstrated no spring or autumn bloom. Species diversity and dominance were stable at the ends of the estuary and fluctuated through the year in midestuary. Species succession differed from regions where one species dominated throughout the year, e.g. Opephora martyi Heribaud at Bowling (high tide), to those where the dominant species was constantly changing e.g. Erskine (low tide). In all 307 species were recorded, twenty-nine very rare, 172 rare, nineteen were abundant, some e.g. Opephora martyi, Navicula mutica var. cohnii (Hilse) Grun. having wide niche breadth (B>60). others being restricted in their distribution e.g. Nitzschia paleacea Kütz. (B=10.4), Navicula pseudocomoides Hendey (B = 14–8). N. mutica var. cohnii and var. mutica Kütz. were difficult to distinguish in terms of valve morphology, as intermediate forms existed. In the estuary, smaller valves occurred towards the freshwater end. Two clones, originating from a 12/μm and a 26 nm valve (length) corresponding to descriptions of var. cohnii and var. mutica respectively, behaved similarly in culture throughout a range of salinity, in terms of size expression, suggesting no taxonomic difference. Diatom community photosynthesis was affected by salinity, reflecting the site of origin.