Rocky reefs provide complex structures in the otherwise largely sand-dominated coastal North Sea. Therefore, these reefs are highly important natural habitats for the functioning of coastal ecosystems, as they provide shelter, refuge and nursery grounds for various mobile and sessile species. In the North Sea, the spatial distribution of these habitats has been intensively investigated over recent years. However, these studies generally provide static accounts of the current state of these reef systems, but limited data exist on the temporal variations in sediment dynamics at and around natural rocky reefs. In this study, we provide observations from a multiannual time series of hydroacoustic seafloor surveys conducted at an isolated rocky reef in the North Sea. We use multibeam bathymetry and side-scan sonar backscatter data in combination with video observations, sediment sampling, and sub-bottom profiler data to assess the long-term variations of the rocky reef system. The reef is located in water depths between 11 and 17 m with an areal extent of ~0.5 km2 and is surrounded by mobile sands. The topography of the rocky reef appears to create a distinct hydrodynamic system that permits mobile sands to settle or move into bathymetrical deeper parts of the reef. Our results suggest a very dynamic system surrounding the reef with large scale scouring, sediment reworking and transport, while the shallower central part of the reef remains stable over time. We demonstrate the importance of hydrodynamics and current scouring around reefs for the local variability in seafloor properties over time. These small-scale dynamics are likewise reflected in the spatial distribution of sessile species, which are less abundant in proximity to mobile sands. The hydroacoustic mapping and monitoring of seafloor dynamics at higher spatial and temporal resolutions presents an important future direction in the study of valuable coastal habitats.