Understanding mechanistic relationships between seagrass and their environmental stressors should be considered for effective management of estuaries and may inform on why change has occurred. We aimed to develop indicators for seagrass health in response to sediment conditions for the Swan-Canning Estuary, south-west Australia. This article describes the development of a new sediment-stress indicator, relating aspects of seagrass productivity with sediment sulfur dynamics. Sulfur stable isotope ratio and total sulfur were measured monthly within the roots, rhizomes and leaves of Halophila ovalis, and significantly varied across sites and months. The growth of seagrass over the summer months appeared restricted by sediment condition, with growth of seagrass lower when sediment derived sulfur and/or total sulfur within rhizome of leaf tissues was higher. H. ovalis appeared quite tolerant of sulfide intrusion within the root compartment, but growth was compromised when sulfide breached the root-rhizome barrier. The tightest correlation between potential sulfur metrics and seagrass growth was observed for the ratio (δ34Sleaf + 30)/(TSleaf), and it is this ratio that we propose may be a useful sediment-stress indicator for seagrass. The study also highlights that sediment condition needs to be considered at the meadow scale.