Changes in relative abundance of estuarine epipelic microalgae along an estuarine gradient were investigated, and population densities of different species along a small-scale nutrient gradient generated by a sewage treatment outfall and in laboratory mesocosms enriched with ammonium were also studied. The relative abundance of certain species of epipelic diatoms was related to location along the estuarine salinity and nutrient gradient: Navicula gregaria and N. phyllepta were abundant at oligo- and mesohaline sites respectively, and Pleurosigma angulatum and Plagiotropis vitrea were abundant at polyhaline sites. On a smaller spatial scale, though there were no significant patterns in microalgal biomass in relation to nutrient enrichment, there were significant differences in the population densities of different epipelic species along a multivariate nutrient gradient (decreasing concentrations of ammonium, nitrite, silicate, organic content, and increasing salinity and pore-water nitrate concentrations) away from a sewage outfall along a saltmarsh creek. The diatoms Nitzschia sigma and Gyrosigma limosum and the cyanobacteria Oscillatoria limosa and O. princeps had significantly higher population densities near the outfall, and Navicula phyllepta, N. pargemina, Nitzschia frustulum, Cylindrotheca signata and Pleurosigma angulatum were significantly more abundant at the seaward end of the gradient. In laboratory tidal mesocosms, sediment cores from along the gradient had their pore-water ammonium concentrations increased to 380–450 μM NH4+. After 26 days, the population densities of Gyrosigma fasciola, G. littorale, P. angulatum, N. phyllepta, Cylindrotheca signata, C. closterium and Niztschia apiculata were significantly reduced, while those of G. limosum, N. sigma, Scolioneis tumida and O. limosa were unaffected, or were significantly higher compared with control cores. Laboratory manipulations of ammonium concentrations supported the observed field distributions, indicating that epipelic species do have different trophic preferences and ammonium concentration may be a significant factor in determining estuarine species composition of epipelic algae.