In intertidal rocky shores, sessile organisms are subject to local variations due to a complex interplay of physical and biological drivers. Here, we examined the patterns and the dynamics of distribution of a key benthic ecosystem-engineer species, the mussel Mytilus galloprovincialis. We characterized areas of loss, gain, and persistence of mussel space occupancy using drone images with a resolution of one centimeter across two rocky shores spanning 3121 m2 and 3499 m2. Then, we assessed the effect of microhabitat slope, microhabitat orientation, and intertidal height on the dynamics of mussel distribution for the two rocky shores. Notably, substantial losses were observed, ranging from 55% to 80% depending on the shore. The hierarchical impact of habitat topographic features on mussel occupancy dynamics diminishes in the order of rocky shore, intertidal height, and microhabitat features. To unravel the dynamics further, we calculated persistence, resilience, and the time to recover from disturbance using a Markov Chain model. Persistence time decreased at the extremes of the rocky shore —both its top and bottom edges. Contrary to expectations, mussels at these edges exhibit higher resilience, preventing their disappearance despite significant losses. Our results not only provide insights into the structural dynamics but also emphasize the need to consider long-term responses to environmental changes. This study underscores the potential of integrating models with drone technology for monitoring intertidal populations, offering a powerful tool to comprehend and anticipate the enduring impacts of environmental shifts on spatial distribution.