This contribution presents the results of a study on the shoreline variability of a natural perched urban beach (Ammoudara, Crete). Shoreline variability was monitored in high spatio-temporal resolution, using TIMEX image mosaics obtained through a coastal video system collecting images at 5 Hz in 10 min bursts every hour with sunlight and analysed through a novel, fully-automated 2-D shoreline detection algorithm. The 10-month monitoring showed that the fronting beachrock reef exerts significant geological control on beach morphodynamics. Cross-shore shoreline change was, in some areas, up to 8 m with adjacent sections of the shoreline showing contrasting patterns of beach loss or gain. Spatial variability increased in spring/early summer, stabilized until the end of the summer when partial beach recovery commenced. Association of the patterns of beach change with the wave forcing (as recorded at an offshore wave buoy) is not straightforward; the only discernible correlation was that particularly energetic waves from the northern sector can trigger changes in the patterns of spatial shoreline variability and that increased variability might be sustained by increases in offshore wave steepness. Hydrodynamic modeling and observations during an energetic event showed that the reef can filter wave energy in a highly differential manner, depending on its local architecture. In some areas, the reef allows only low energy waves to impinge on the shoreline, whereas elsewhere penetration of higher waves is facilitated by the low elevation and limited width of the reef or by the presence of an inlet. Wave/reef interaction can also generate complex circulation patterns, including rip currents that appeared to be also constrained by the reef architecture.