Differences in phosphorus (P) availability can influence the ecology and physiology of seagrass communities; and are usually inferred from changes in the relative P content in seagrass leaves. Shark Bay is a subtropical marine embayment, with decreasing P concentrations in the water column and sediments from north to south across the entire embayment. We examined the P and nitrogen (N) content of seagrass leaves and P content of sediments across the Faure Sill and Wooramel delta region of Shark Bay, to determine whether the leaf content of seagrasses in Shark Bay also decreased from north to south over smaller spatial scales. Nutrient content of Amphibolis antarctica and Halodule uninervis were highly variable and were not strongly correlated with sediment P concentrations. Mean N : P ratios of seagrasses (<33.5) were not indicative of P limitation, as has been previously assumed for Shark Bay. We conclude that availability of P for uptake by seagrasses across Shark Bay may be highly localised and cannot be predicted from system-scale gradients (>100 km) of sedimentary P distributions. We suggest that P availability to seagrasses is more likely a complex function of differing nutrient inputs, rates of delivery to the plants and cycling rates.