Anthropogenic stressors and global change have led to many tropical seagrass meadows switching to dynamic early-successional states exhibiting widescale patchiness. Previous experimental evidence has suggested that when patchiness in vegetated ecosystems is driven by positive feedbacks, it can be used as an indicator for resilience. Testing the efficacy of patchiness as a resilience indicator for seagrass meadows, we integrated field measurements with drone and satellite imagery to examine both the spatial and temporal dynamics of segrass meadows in the Derawan Archipelago, Indonesia over 10 years. By quantifying how the spatial characteristics of meadows across Derawan have changed and identifying the main drivers of this change, we showcase how multiple stressors combine to reduce the resilience of these seagrass meadows. While a large turtle population initiates seagrass meadow patchiness through grazing, increasing local anthropogenic stressors exacerbate the level of patchiness, putting the meadows at risk to further disturbance. Combining a mechanistic understanding with a large spatial dataset obtained from aerial and satellite imagery, we detail how ecosystem dynamics within seagrass meadows can be disentangled to evaluate the ecosystems’ resilience, thereby providing a novel approach to effectively monitor and protect seagrass ecosystems.