In the context of industrial-era global change, Mediterranean coastal areas are threatened by relative sea level (RSL) rise. Shifts in the drivers of coastal dynamics are forecasted to trigger changes in the frequency of flooding of low-lying areas, with significant effects on marine-coastal environments, societies, economy and urban systems. Here, we probe coastal floods in the eastern part of the Gulf of Venice (coastal Croatia) to understand the drivers of saltwater intrusions. We reconstructed RSL rise in the north-eastern Adriatic during the Holocene based on 43 RSL index points and analyzed the evolution of coastal submersions on the Istrian Peninsula for the last 5200 years based on inputs of marine components and increases in supratidal scrubs. We produced pollen-based climate reconstructions to analyze the potential effects of air temperature and precipitation changes on submersions. We investigated the response of precipitation and temperature to mid-late Holocene summer/winter insolation forcing and insolation-induced changes in sea surface temperatures (SSTs). We found that during periods of warmer SST, coastal flooding increased markedly. This process seems to have been initiated by warmer atmospheric temperatures that led to increases in summer evaporation, counterbalancing the effects of heavy precipitation during winter. As a result, freshwater flows into coastal areas were reduced and resulted in recurrent inputs of saltwater inland. Our study suggests that present-day climate drivers (increases in SSTs and air temperatures, and decreases in precipitation) will probably favour frequent coastal flooding, a process that will be amplified by RSL rise.