Seagrass meadows commonly occur near ports and urban centres, exposing them to increased risks and threats associated with anthropogenic activity. Effectively mitigating these risks requires a strategic approach to monitoring condition and resilience, and the development of appropriate management tools. This approach has been applied in the Ports North/JCU Seagrass monitoring program which has examined seagrass habitats in the port, as well as a range of targeted research for management application for the past 21 years. As part of this program, we conducted a targeted study on the sediment seed bank of Cairns seagrasses in response to meadow-scale seagrass loss, and concerns raised over their capacity for recovery and resilience. A spatially explicit seed bank analysis was paired with a long-term annual assessment of seagrass distribution to assess seed bank spatial patterns and their relationship with fuelling the recovery and presence of seagrass. Results demonstrated that the Cairns Harbour seed bank was not uniform and had a species dependent spatial and temporal structure related to previous seagrass distribution. Measurements of seed-bank viability over time demonstrated a rapid decline of seed viability following the seagrass loss and no replenishment. Recovery of the meadows occurred from the few viable seeds that remained 3-4 years after loss. The seed bank did not provide a static level of insurance distributed evenly across entire meadows and in the event of meadow scale loss there is a limited temporal capacity to generate recovery. Understanding these spatial, temporal and species-specific dynamics adds valuable context for management of seagrasses, especially for decisions on interventions such as restoration and informing recovery.