This paper emphasises an ionic composition of the pore water of bottom sediments and subsea permafrost as an indicator of salinization of the thawed strata. Based on measurements of concentration of sodium (Na+), potassium (K+), calcium (Ca2+), and magnesium (Mg2+) cations, chlorides (Cl–) and sulphates (SO42–) in water extracts from bottom sediments and subsea permafrost deposits from three boreholes, a spatial difference in salinization of thawed strata within the Buor-Khaya Bay was shown. The vertical pattern of the macroions in the unfrozen segment was formed under subsea thawing of permafrost. The frozen strata contain fresh pore water and have been evolving under downward penetration of salt and subsequent thawing of subsea permafrost. Based on the analyses of thawed deposits, it was shown that the maximum pore water salinity was observed in the horizons enriched with sand and plant detritus. Over the boundary of subsea permafrost in the Ivashkina Lagoon, the pronounced total ion concentration (up to 50 g/L of Cl–) of pore water was observed. This segment consists of moss debris, which is characterised by high porosity. The moss layer promotes the accumulation of dissolved pore water compounds and subsequent thawing of the frozen sediments.