The seagrass Amphibolis antarctica is an important component of coastal soft-sediment ecosystems across southern Australia. Large-scale losses of A. antarctica at several locations have been linked to anthropogenic nutrient inputs. The present study comprised a field survey to test whether the spatial patterns of plant biomass, canopy structure and epiphyte biomass in A. antarctica could be predicted based on expectations related to nutrient status across two regions within Gulf St Vincent, South Australia. Specific predictions were that: (1) plant biomass, plant density, plant height, leaf cluster frequency and leaf frequency are all lower in the east (higher nutrient) region than in the west region; and (2) epiphyte biomass and epiphyte load are higher in the east than in the west. Regional nutrient status was a poor predictor of most of the parameters measured, with the opposite trends to those predicted often occurring. Plant biomass, canopy structure and epiphyte biomass appear to be a result of several site-specific factors that are not fully understood at this time. The results of the present study have significant implications for making generalised predictions and for monitoring A. antarctica on urbanised coasts, and will also be useful for informing ecological studies on plant–epiphyte and plant–animal interactions in A. antarctica ecosystems.