Coral reefs are subject to numerous physical disturbances, and post-disturbance coral recovery potential depends on subsequent re-colonization of impacted habitat. We examined divergent recovery trajectories at 2 proximal reefs disturbed by ship groundings that resulted in clearly delineated areas of altered substrate. Post-disturbance measurements of coral recruitment, survival, and changes in community structure were made approximately annually from 2009-2013 in undisturbed reference areas as well as disturbed pavement and rubble areas. Despite similar initial physical disturbances, there were marked differences between sites, with higher coral recruitment and survival on disturbed pavement than rubble bottom, reference reef, or restoration structures. Subsequent episodic disturbances from rubble mobilization could be a mechanism driving the divergent recovery patterns. To estimate whether local hydrodynamic conditions were sufficient to mobilize rubble, we used a combination of long-term monitoring, hydrodynamic modeling, and rubble transport mechanics to hindcast the potential for substrate mobility. Long-term model simulations of hydrodynamic forcing at the study sites showed multiple events where bottom-orbital velocities exceeded thresholds required to mobilize rubble via sliding or overturning. Our analyses indicate that wave energy mobilizes rubble substrate multiple times annually and suggests a physical limitation on survival of coral recruits relative to those on pavement substrate. Continued mobilizations may establish a positive feedback loop in which continued rubble clast mobilizations cause additional mechanical erosion or breakage and a shift to smaller rubble sizes that would subsequently mobilize at a lower level of hydrodynamic forcing and thus become subject to more frequent and sustained disturbances. The combination of multiple hydrodynamic disturbances and unstable substrate limits coral recovery and thus contributes to prolonged habitat loss