AbstractAs β‐diversity can be seen as a proxy of ecological connections among species assemblages, modeling the decay of similarity in species composition at increasing distance may help elucidate spatial patterns of connectivity and local‐ to large‐scale processes driving community assembly within a marine region. This, in turn, may provide invaluable information for setting ecologically coherent networks of marine protected areas (MPAs) in which protected communities are potentially interrelated and can mutually sustain against environmental perturbations. However, field studies investigating changes in β‐diversity patterns at a range of spatial scales and in relation to disturbance are scant, limiting our understanding of how spatial ecological connections among marine communities may affect their recovery dynamics. We carried out a manipulative experiment simulating a strong physical disturbance on subtidal rocky reefs at several locations spanning >1000 km of coast in the Adriatic Sea (Mediterranean Sea) and compared β‐diversity patterns and decay of similarity with distance and time by current transport between undisturbed and experimentally disturbed macrobenthic assemblages to shed light on connectivity processes and scales involved in recovery. In contrast to the expectation that very local‐scale processes, such as vegetative regrowth and larval supply from neighboring undisturbed assemblages, might be the major determinants of recovery in disturbed patches, we found that connectivity mediated by currents at larger spatial scales strongly contributed to shape community reassembly after disturbance. Across our study sites in the Adriatic Sea, β‐diversity patterns suggested that additional protected sites that matched hotspots of propagule exchange could increase the complementarity and strengthen the ecological connectivity throughout the MPA network. More generally, conditional to habitat distribution and selection of sites of high conservation priority (e.g., biodiversity hotspots), setting network internode distance within 100–150 km, along with sizing no‐take zones to cover at least 5 km of coast, would help enhance the potential connectivity of Mediterranean subtidal rocky reef assemblages from local to large scale. These results can help improve conservation planning to achieve the goals of promoting ecological connectivity within MPA networks and enhancing their effectiveness in protecting marine communities against rapidly increasing natural and anthropogenic disturbances.