Permafrost, or perennially frozen ground, and seasonally frozen ground in the Arctic modulate many processes such as landscape stability, hydrological conditions, and biogeochemistry of terrestrial and aquatic ecosystems. Permafrost conditions across the Arctic are changing due to climatic impacts like warming and hydrological intensification. Ocean dynamics such as sea level rise, sea ice loss, and increasing ocean surge frequency further threaten coastal permafrost through saltwater intrusion and increased erosion. Across the globe, saltwater intrusion has ecological and biogeochemical consequences, with additional implications for soil freezing point depression in high latitude environments. Models have identified some impacts of flooding and saltwater intrusion on coastal Arctic soil thermal conditions, however, integrative approaches are needed to understand the feedbacks between coastal flooding, tundra degradation, and permafrost thaw in situ. To assess consequences of saltwater intrusion in a coastal Arctic system, we used a combination of pore water salinity, thaw depth, multi-depth temperature probes, and geophysical methods, including electrical resistivity tomography and multi-frequency electromagnetic surveys. Areas with increased pore water salinity had degraded vegetation and greater active layer thickness. Geophysical surveys showed these areas had pronounced differences in ice-rich permafrost distributions, demonstrating the long-term impacts on coastal stability. Yearlong time series of soil temperature profiles across degradation states revealed further differences in soil thermal properties at both diel and seasonal scales. For example, vegetated sites had up to 10°C cooler temperatures than the degraded sites throughout the soil profile during summer. We demonstrate that in addition to freezing point depression, feedbacks between ecological conditions or soil properties complicate the impacts of coastal flooding and saltwater intrusion across much of the coastal Arctic. Integrating multiple methods is critical for achieving a process-based understanding of the effects of saltwater intrusion on interacting ecological, hydrogeological, and thermal processes along permafrost-bound coastlines.