In this study, we used orthomosaics and a digital surface model (DSM) generated from drone surveys to (1) characterize the distribution of mussel (Mytilus galloprovincialis) aggregations at high resolution (centimeters), and (2) evaluate the role of topographic features, intertidal height, slope, and orientation angle in determining mussel distribution on two rocky shores oriented differently on both sides of a beach on the French Brittany coast. We first developed and tested a mussel visualization index (MVI) for mapping mussel aggregations from drone images. Then, we analyzed mussel distribution on the two shores. The results showed a contrasted total mussel-occupied area between the two rocky shores, with a higher occupation rate and a clear pattern of distribution depending on topographic features on the rocky shore oriented to the west. Intertidal height, and its associated immersion time, was the main factor determining mussel distribution. An optimum intertidal height was found in the center of the distribution height range, at c.a. 4.5 m above the lowest astronomical tide (LAT), where individuals are under immersion phase on average 43% of the time. Within this optimum, the occupation rate of the mussels was significantly higher in microhabitats facing south and west, particularly at intermediate slope angles. These results demonstrate the role of microhabitat topographic features on the development of intertidal mussels and their final distribution. Furthermore, the results highlight the importance of mesoscale structures of habitats (e.g., 100 m), which seem to be responsible for the differences we observed between the two shores. Our methodological approach highlights the main advantage of using high-resolution drone images to address ecological processes in intertidal ecosystems. Indeed, drone imagery offers the possibility to assess small-scale interactions between individuals and habitat conditions over a wide area, which is technically infeasible from fieldwork approaches or by using satellite remote sensing due to their lower resolution. Scale integration and methodological complementarity are powerful approaches to correctly represent the processes governing the ecology of intertidal ecosystems. We suggest using this methodology to monitor long-term changes of sentinel sessile species.