Intertidal cohesive estuarine sediments frequently support extensive microphytobenthic biofilms, which are usually dominated by epipelic (motile) diatoms. The distribution of different diatom taxa varies along estuarine gradients, but it is not clear what the causative factors are in determining these patterns. In many estuaries, salinity covaries with other environmental gradients, particularly with nutrient concentrations when the river is the main nutrient source. Autecological information is required to aid interpretation of these field distributions. In this study the maximum specific growth rate (μ) and stationary phase biomass of four common taxa of estuarine epipelic diatoms (Navicula phyllepta, N. perminuta, N. salinarum and Cylindrotheca closterium) were measured in axenic unialgal cultures grown under a range of nitrogen and salinity regimes. All three Navicula species and two different clones of C. closterium showed significant differences in their response to a range of ammonium (10–4000 μM) and nitrate (10–2000 μM) concentrations across a salinity range of 10–35‰. Growth rates of N. phyllepta were significantly lower at ammonium concentrations > 400 μM, but the other three taxa showed little evidence of ammonium toxicity, even at concentrations > 1 mM. On the basis of the response of each species, the following putative ranking of preferences for inorganic nitrogen concentrations (lowest to highest, with salinity optima in parentheses) was constructed: N. phyllepta (10–20‰) – N. perminuta (10–30‰) – N. salinarum (20–35‰)/C. closterium (clone 1, 10–25‰, clone 2, 25–35‰). Such a ranking should be interpreted cautiously, as interclonal differences and adaptation to local environmental conditions can alter the preferences of taxa. These autecological data are partially supported by previously published data on field distribution, and suggest that certain taxa may have value as trophic indicator species.