Loss of seagrasses caused by mooring damage at Rottnest Island, Western Australia, was studied using aerial photographs taken between 1941 and 1992. The temporal decline of seagrass beds damaged by moorings was studied by comparing areal coverages of seagrasses and sand patches, and increases in the length of the exposed seagrass edge within seagrass beds. The study concentrated on Rocky Bay and Thomson Bay where the bulk of permanent moorings are located. Rocky Bay is more exposed to the prevailing westerly swell direction and Thomson Bay is a protected east facing bay. The loss of seagrasses associated with moorings in Rocky Bay has been dramatic, with 18% of seagrass area lost between 1941 and 1992, and 13% between 1981 and 1992. The exposed edge of the beds increased by 230% between 1981 and 1992. Sand patches associated with moorings have coalesced in the shallow central west part of the bay. The change from single weighted swing moorings to three chained cyclone moorings has resulted in greater loss of seagrasses. Single cyclone moorings produce three circular holes in the seagrass bed. The areal loss recorded from Thomson Bay was less than 5%, yet the exposed edge of the seagrass beds doubled between 1941 and 1992. Fragmentation of the bed was visible near heavy use areas. Some regrowth was recorded to the north of the main ferry jetty where the sedimentary environment is depositional. The effects of moorings on seagrasses at Rottnest Island varied from devastating in Rocky Bay to small in Thomson Bay. The differences seem to be related to exposure to prevailing swell and whether the environments are erosional or depositional. Thus a single management protocol, such as cyclone moorings versus swing moorings, is inappropriate. Physical environments need to be assessed before determining the number and types of moorings allowable in bays at Rottnest Island.