Carbon and nitrogen stable isotope ratios of three estuarine autotrophs (the seagrass, Zostera capricorni and its epiphytic algae, and the saltcouch grass Sporobolus virginicus) were measured within and among sites in Southern Moreton Bay, Southeast Queensland. For all taxa, isotope ratios were significantly affected by the position of a plant within a site. Carbon signatures of S. virginicus were more enriched at upper elevations (-14.3马 and more depleted at the lower edge (-15.0驮 Small but significant differences for S. virginicus were also found between edge (-14.7驠and interior (-14.9驠positions. Z. capricorni was more depleted in 15N at edge (5.9驠positions than the interior (6.2驮 The seagrass epiphytes varied along the elevation gradient, being more depleted in 13C at the upper (-19.7驠than the lower (-19.3驠edge. This small within-site variation (< 1驠may result from differences in the physical characteristics among the sites that influence the productivity of plants and thereby their isotope ratios, but would not preclude the use of carbon and nitrogen stable isotopes in small-scale food web studies. At a larger scale, isotope ratios differed significantly among sites separated by several kilometres and the range of this variation was greater for all taxa than at the within-site scale. Differences among sites are probably due to variation in nutrient source and hydrodynamics.