Many low-lying coastlines are exposed to overwash and marine flooding during large wave events and the role of coastal ecosystems in reducing these hazards is more and more cited. The proposed article deals with the assessment of processes involved in runup-induced coastal flooding over two years and 10 months at Anse Maurice, a reef-fringed pocket beach located in Guadeloupe Island, in the Caribbean region. Daily maximum marine inundation was assessed using a fixed video system and two hydrodynamic measurements campaigns were organised to monitor local wave transformation through the reef system. Daily Highest Runups (DHR) remains primarily correlated to individual storm events as extreme runups are observed in correlation with storm swells. However, results evidenced that storm runup intensity is highly modulated by (1) the annual periodicity of sea level (24% of the global runup variability) showing minimums in May and maximums in November and (2) the tidal level influencing short waves and infragravity waves propagation into the reef flat. Those variabilities determine the reef submergence, an important parameter involved in wave transformation over reefs. This leads to different runup responses for similar incident wave conditions. For example, most of the winter storm events only induce moderate intensity runup while cyclonic events with the same swell intensity generate more extreme runups. The upperbeach vegetation also clearly influences the maximum swash excursion at the beach and potential back beach flooding by swash processes. This study brings new comprehensive elements on runup beahavior and nearshore processes at different timescales on reef-lined beaches.