We investigated seagrass species distribution and nutrient content in the iconic phosphorus-limited Shark Bay, Western Australia. We found the slower-growing, temperate species Amphibolis antarctica and Posidonia spp. had lower N and P content compared to the faster-growing tropical species Halodule uninervis, Syringodium isoetifolium,Cymodocea angustata, Halophila ovalis and Halophila spinulosa. Further, by comparing elemental content of different seagrass species at sites where species co-occurred, we were able to standardize seagrass elemental content across sites with different species composition. This standardization allowed us to make ecosystem-scale inferences about resource availability despite taxon-specific distributions and elemental content. We found a marked spatial pattern in N:P of seagrasses across the system, indicating that P limitation occurred, despite calcium carbonate sediments, only in the most isolated portions of the bay. Large areas closer to the mouth of the bay were either N limited or were not limited by N or P availability. Our results suggest that large-scale nutrient budgets may oversimplify our understanding of limiting factors in a system, resulting in management decisions that may have unforeseen effects on different areas within the same ecosystem.