Flooding of low-lying Arctic regions has the potential to warm and thaw permafrost by changing the surface reflectance of solar insolation, increasing subsurface soil moisture, and increasing soil thermal conductivity. However, the impact of flooding on permafrost in the continuous permafrost environment remains poorly understood. To address this knowledge gap, we used a combination of available flooding data on the Ikpikpuk delta and a numerical model to simulate the hydro-thermal processes under coastal floodplain flooding. We first constructed the three most common flood events based on water level data on the Ikpikpuk: snowmelt floods in the late spring and early summer, middle and late summer floods, and floods throughout the whole spring and summer. Then the impact of these flooding events on the permafrost was simulated for one-dimensional permafrost columns using the Advanced Terrestrial Simulator (ATSv1.0), a fully coupled permafrost-hydrology and thermal dynamic model. Our results show that coastal floods have an important impact on coastal permafrost dynamics with a cooling effect on the surficial soil and a warming effect on the deeper soil. Cumulative flooding events over several years can cause continuous warming of the deep subsurface but cool down the surficial layer. Flood timing is a primary control of the vertical extent of the permafrost thaw and the active layer deepening.