Critical habitats within estuaries such as seagrass are experiencing high concentrations of impacts. Increasing urbanisation, warming and poor water quality have caused a global seagrass decline of 8% per year. However, seagrass is ephemeral by nature, and patches often shift or reappear nearby. Due to the ephemeral nature of seagrass distribution identifying whether seagrasses are under stress remains a substantial challenge for managers. Traditional seagrass health metrics include aerial extent, canopy height, above ground biomass or densities. By the time these metrics detect a decline, recovery may be impossible. Identifying sub-lethal stressors is imperative in effective proactive management. During periods that do not facilitate photosynthetic activity such as storm surges or winter months seagrasses rely on non-structural carbohydrate reserves in their rhizomes. Resiliency can therefore be inferred based on levels of non-structural carbohydrates. This study uses thermal outflows associated with power stations in a large NSW estuary as a proxy for a future climate change scenario to investigate the effects of sub-lethal temperatures in situ on the common seagrass species Zostera muelleri. If thermally affected areas have significantly lower levels of non-structural carbohydrates than control locations this implies that warming may facilitate lowered resilience of seagrass to future stress events.