Seagrasses are subjected to intense levels of anthropogenic disturbance as a result of the shallow nearshore waters they inhabit. Some seagrasses are known to have dynamic growth patterns, enabling them to colonize unstable shallow environments and adapt to a range of disturbances. This can result in high levels of variability in morphological and physiological attributes. The seagrass Halodule wrightii is known to be a fast-growing pioneering species with a large geographic range. The present study examines Halodule wrightii in a region under intense anthropogenic stress in order to determine what are the main environmental drivers affecting the morphology, physiology and status of these habitats. Parameters of plant morphology, physiology and status were measured either at the meadow scale (e.g. biochemistry) or at a higher frequency shoot scale (e.g. shoot width). We assigned an impact assessment index to a series of seagrass sites over a gradient of anthropogenic disturbance and found this to be explanatory of a number of the seagrass parameters measured including epiphyte cover, stable isotope δ15N and ETRmax however, it did not clearly explain shoot density, a commonly used bioindicator of environmental stress. At the shoot scale, Principal Component Analysis identified epiphyte and leaf width to have the strongest association. At the meadow scale this was shoot density, dry weight and Ek, albeit with the most impacted sites showing highest shoot density. Stable isotope (δ15N) and leaf length were most significant in explaining the variation between sites and impact category, providing a direct link between anthropogenic sources of nutrients to seagrass meadow density.